Data format: ----------- Column 1 is genename, last column is the signal at t=0 (normalized w.r.t. median of the slide) and rest of the columns are percentage difference in signal from t=0. Col. 2= (t30-t0)/t0, Col. 3=(t45-t0)/t0, Col. 4=(t120-t0)/t0. WARNING: ------- Before you make a judgement based on the percentages in column 2, 3, 4, always check column 5. If the number in column 5 is too small, may be the gene is not expressed and all we are picking up are variations in noise. For comparison, here are similar information on 21 randomly picked genes. Real data starts below this table. 171282 -4.24% -10.2% 0.56% 1.17 153085 6.76% -13.5% -3.39% 0.73 170932 15.57% 7.53% 2.49% 0.99 152963 -31.45% -29.29% -34.06% 1.15 157184 -9.64% -7.2% 14.74% 0.81 171962 23.77% -11.69% 16.86% 0.66 167309 4.27% -37.77% -23.03% 1.75 164658 -8.9% -17% 29.08% 1.23 162564 -8.42% -19.22% 0.6% 1.15 157482 0.39% 4.88% 9.75% 0.66 159414 -5.94% -19.13% 9.89% 1.97 158830 -13.7% -0.96% -1.94% 1.01 170062 -4.16% -8.05% -8.13% 0.77 160518 -4% 16% -14.7% 0.75 160388 11.17% -11.16% 3.45% 0.93 165045 0.15% 8.92% 12.03% 1.59 156681 -1.98% -22.83% 8.41% 1.12 167940 34.43% -18.57% 21.57% 1.82 155554 -5.96% 4.65% 56.97% 0.65 159393 -31.94% -30.87% 35.62% 4.64 159026 36.24% -2.73% 21.38% 1.34 I. gene lists to compare the microarray expression data with prior studies of gene expression. I. A. genes that are upregulated upon deflagellation in Chlamydomonas the first 22 genes are taken from various previously published studies of regeneration using Northern blots. The rest are taken from Li and Dutcher's comparative genomics paper in which they used RT-PCR to analyze a set of candidate genes. 167398 -20.88% -15.26% -11.58% 2.31 outer dynein arm light chain DLC5 14,000kDa patel-king et al 1996 157642 -14.71% -14.71% -2.16% 1.3 168923 -5.69% 34.6% -30.05% 1.31 PF6 158670 -4.1% 16.43% 7.14% 0.73 159590 -1.86% -27.63% -1.13% 1.31 165162 -0.4% -11.64% 2.73% 1.24 ODA5 154949 1.44% 23.07% -9.97% 1.04 169516 1.63% 4.81% -7.89% 0.62 (a.k.a. DHC2 dynein heavy chain) 169489 6.84% 0.55% -8.35% 0.95 160023 7.67% 9.58% -5.41% 1.04 159662 10.92% 0.2% -0.61% 1.21 FA1 152526 11.12% 30.17% 2.65% 0.94 159573 17.95% 0% 2.27% 1.16 157246 19.49% 20.12% 27.04% 0.79 157793 23.53% 26.8% 6.53% 0.76 163484 24.01% 15.86% -4.08% 1.1 165091 25.05% -11.38% 42.59% 2.41 169293 25.39% 9.84% -16.11% 0.96 165004 25.85% 31.32% 5.78% 0.82 165537 26.69% 53.37% -10.14% 0.44 168565 30.25% -4.18% -14.56% 0.79 153422 31.21% 6.02% -6.38% 1.32 161738 34.31% 42.88% -15.27% 1.04 156365 34.96% 0.3% 68.69% 1.64 165684 37.54% -7.14% -6.4% 1 169882 41.2% 13.25% 9.73% 1 162929 43.73% 51.14% 11.12% 0.67 171797 46.3% 12.96% 39.77% 1.07 153053 47.19% 23.29% -1.24% 0.79 166686 47.8% 6.44% 13.89% 1.47 156513 50.04% 21.46% 0.48% 0.83 156513 50.04% 21.46% 0.48% 0.83 KPL2 induced during mammalian trachael ciliogenesis 159155 54.96% 27.24% -13.87% 1 158615 60.01% 40.31% 8.66% 0.83 158194 61.09% 45.16% 0.6% 0.84 Fla10 168165 65.75% 21.69% 38.12% 0.71 158752 65.8% -6.03% -4.31% 1.73 158033 71.88% 66.67% -8.88% 0.47 163664 74.46% 23.13% 1.15% 1.53 157052 76.19% 40.82% -5.26% 0.74 MBO2 153708 81.06% 27.19% 12.12% 1.1 LF4 164660 83.81% 1.44% 30.93% 1.07 163277 91.26% 41.44% -14.82% 1.12 165115 91.7% 79.72% 11.98% 0.83 166736 92.65% 42.85% 3.51% 1.22 IC140 (IDA7) 164264 100% 22.26% -23.52% 0.84 167776 110.06% 37.1% 33.84% 0.79 156043 116.06% 48.75% 9.94% 1.3 164149 117.95% 77.94% 6.19% 0.72 166131 118.52% 43.45% 31.97% 0.97 PF20 157798 127.93% 33.57% 1% 0.75 ODA3 164561 129.22% 93.45% 24.46% 1.36 158863 134.99% 49.99% -2.5% 0.8 162279 143.86% 56.65% 6.06% 0.95 Rsp3 171911 153.4% 43.84% -9.11% 0.88 163193 161.35% 80.24% -6.28% 1.1 154393 168.36% 81.09% 5.86% 1.36 IFT52 164100 170.31% 81% 4.73% 0.83 IC70 (a.k.a. ODA6) 165905 171.6% 142.27% -4.57% 0.78 153853 196.25% 75.98% 7.61% 0.78 159749 212.19% 180.48% 37.7% 1.23 153658 220.27% 157.04% -1.71% 0.72 161253 221.12% 27.38% 2.99% 1.58 156948 232.55% 56.82% 19% 0.89 IFT57 171602 302.64% 147.04% 109.3% 0.62 159247 334.95% 35.71% -20.73% 0.61 164620 345.71% 192.45% 114.43% 10.55 alpha-1 tubulin (probably the most strongly induced known gene) 157968 354.54% 140.72% 5.27% 1.37 RSP6 171096 367.77% 123.03% -4.21% 1.51 PF16 160297 371.12% 219.34% 83.35% 1.13 157967 382.67% 240.87% 30.47% 1.06 RSP4 165606 389.99% 208.84% 67.13% 1.58 170055 418.67% 214.58% 97.42% 8.7 beta-2 tubulin 171102 431.1% 197.22% 16.93% 1.04 168339 443.1% 126.61% -7.46% 0.66 160952 676.09% 213.18% 43.84% 1.19 DC3 (outer arm docking complex subunit DC3) 162703 724.23% 436.64% 87.7% 1.73 I. B. genes that are known NOT to be upregulated after deflagellation the first four are taken from published studies of gene expression during regeneration using Northern blots. The rest are from the systematic RT-PCR analysis of Li and Dutcher. 158239 -45.89% -46.98% -24.85% 1.82 166667 -41.33% -47.33% -47.79% 1.49 171242 -39.75% -9.63% 105.39% 0.82 164197 -35.7% -33.27% -25.64% 1.43 171299 -35.25% -27.41% -33.95% 1.52 166414 -31.76% -24.31% -1.74% 4.29 158560 -27.97% -35.55% 29.5% 2.37 168391 -25.38% -32.96% -1.52% 104.76 RBCS2 (should be an abundant transcript in all samples) 162000 -21.88% -37.58% 56.8% 1.36 169942 -21.45% -24.52% -18.7% 1.62 158402 -19.33% -26.86% 5.77% 0.92 165846 -19.08% 2.27% -16.83% 0.88 161792 -18.1% -27.43% -22.81% 0.96 165904 -18.1% -51.04% -3.18% 60.52 CRY1 S14 ribosomal protein (RPS14) [the most commonly used ctrl] 165247 -17.46% -50.04% -21.45% 52.77 Cblp (chlamydomonas beta subunit-like polypeptide 162224 -16.43% -32.88% -2.81% 2.21 156229 -16.27% -2.31% -18.13% 1.07 162018 -16.06% -21.6% -21.05% 1.8 165072 -13.38% -58.89% -37.67% 18.17 aldolase (note I corrected the ID from the first list) 165102 -12.77% -8.36% -3.96% 1.13 154013 -12.36% -10.5% 30.87% 2.68 168343 -10.34% -10.97% 12.15% 1.59 162907 -10.07% 40.77% -23.24% 0.93 164928 -7.92% -28.11% 3.07% 1.63 156671 -7.83% -22.75% 3.93% 1.13 157385 -7.8% -9.36% -18.8% 0.63 159566 -7.57% -25.11% 37.68% 2.1 162058 -7.21% -4.31% -0.47% 1.03 168715 -6.38% -14.89% -5.41% 0.94 155468 -5.1% 25.83% 2.75% 0.72 155925 -5.1% 26.12% 9.2% 1.61 161779 -4.58% -19.44% 17.62% 1.27 165569 -4.24% 13.55% -5.78% 0.81 166774 -3.69% -20.98% 15.43% 0.8 163738 -3.54% -12.68% -10.14% 0.98 169453 -3.39% -5.87% 6.62% 1.61 155451 -3.06% -7.51% 8.34% 0.89 171166 -1.98% 2.02% -12.48% 0.99 167803 -1.66% -1.66% -4.38% 0.74 167053 0% -12.03% 9.74% 0.66 156530 0.43% -13.81% 73.01% 1.47 154789 0.55% 1.07% 13.04% 0.95 170673 0.68% 2% -5.95% 0.75 156598 1.28% 13.94% -3.15% 0.78 155817 2.39% -41.05% 2.15% 1.16 164517 3.45% 22.26% 2.58% 0.58 157943 4.57% 7.35% -3.54% 1.26 168286 6.17% 9.26% -6.48% 0.8 153859 6.34% -19% 28.05% 1.41 171684 10.76% 8.41% 4.88% 1.27 155464 13.31% -21.39% -21.49% 0.97 166044 14.63% 15.19% 1.14% 0.88 160951 16.88% 19.13% -1.15% 0.88 164610 19.07% -5.11% 1.39% 1.07 164333 19.68% 5.51% 6.29% 0.95 168283 20% 2.97% -6.13% 1.26 164774 20.01% 18.47% 21.39% 0.64 159111 28% 18.85% 23.4% 0.87 164526 56.59% 16.79% 5.31% 0.76 I. C. gene that should not be expressed AT ALL in this strain 156490 24.37% 75.93% 2.35% 0.32 FUS1 (mating type + specific gene, samples are from mt- lack FUS1) II. Genes for which the localization of the gene product is known with respect to flagella in Chlamydomonas. Once the lists in section I are analyzed to show that the microarray method can mostly reproduce known expression patterns (i.e. a control for the technical methodology), an analysis of these lists will confirm our overall strategy of using gene expression as a way to identify likely flagellar components. II. A. gene products known to localize to flagella in Chlamydomonas 167398 -20.88% -15.26% -11.58% 2.31 DLC5 outer dynein arm light chain 5 (14 kDa dynein light chain) 168923 -5.69% 34.6% -30.05% 1.31 PF6 central pair microtubule protein 169341 -3.46% 10.84% 3.28% 1.22 FMG1A flagellar membrane glycoprotein 1A 171599 -3.27% 4.97% -10.14% 0.9 DHC11 inner arm dynein heavy chain 11 161326 -3.09% 4.45% -8.76% 0.79 DHC7 inner arm dynein heavy chain, N-terminus (split gene model) 161759 -2.89% -8.67% -1.45% 1.21 DHC3 dynein heavy chain 3 (inner arm?) C-terminus 162594 -1.1% 11.69% 5.29% 0.85 DHC4 inner arm dynein heavy chain 4 165162 -0.4% -11.64% 2.73% 1.24 ODA5 associated with flagellar adenylated kinase 169516 1.63% 4.81% -7.89% 0.62 DHC1b cytoplasmic dynein 1b heavy chain (retro IFT) 152507 3.11% -15.55% 49.82% 1.12 EB1 MT +end tracking protein (Pedersen et al) 171127 5% 1.88% -6.26% 0.79 DHC2 inner arm dynein heavy chain 2 161758 5.47% 11.53% -3.66% 0.82 DHC3 inner arm dynein heavy chain 3 163907 6.62% 12.65% 2.7% 0.82 DHC6 inner arm dynein heavy chain 6 167981 7.22% -4.11% -3.08% 0.96 KAT2 katanin p60 subunit 162407 9.2% 7.97% 2.43% 0.81 DHC5 inner arm dynein heavy chain 5 159662 10.92% 0.2% -0.61% 1.21 FA1 flagellar autotomy protein 169338 11.36% 16.8% 5.48% 1.1 FMG1b flagellar membrane glycoprotein 1b 169191 11.47% 12.53% 22.66% 0.93 DHC9 inner arm dynein heavy chain 9 156655 12.38% 4.52% -0.53% 0.88 RSP2 radial spoke 2 (annotaed by lefebvre) which is right? 153086 14.09% 6.44% -15.54% 0.78 FA2 Nek kinase 171231 14.15% -11.5% 11.01% 1.12 LF3 reported to downregulate during regen 158922 15.01% 4.81% -5.95% 0.88 IDA2 inner arm dynein 1 heavy chain beta (DHC1-beta) 168520 17.18% 9.41% 1.96% 0.77 ODA11 outer dynein arm heavy chain alpha 154251 27.86% 34.42% 9.6% 1.06 MST1 mastigoneme protein 1 153556 28.78% 12.12% 12.87% 0.66 DHC1 inner arm dynein 1 heavy chain alpha (DHC1-alpha, PF9) 161325 33.96% 16.82% 5.39% 0.78 DHC7 inner arm heavy chain 7 C-terminus 157469 34.33% 14.93% 7.46% 1 ODA2 outer arm dynein heavy chain gamma 168243 40.74% 38.52% 3.7% 0.67 IFT140 160289 43.92% 22.11% -0.94% 0.8 ODA4 outer dynein arm heavy chain beta 158273 51.77% 13.04% 1.35% 1.26 DLC4 outer dynein arm light chain 4 (18 kDa light chain) 157911 59.1% 44.48% -4.07% 0.85 IFT172 158194 61.09% 45.16% 0.6% 0.84 FLA10 kinesin-II subunit for IFT 157405 66.96% 21.54% 2.66% 0.78 FLA8 kinesin-II subunit for IFT 160144 70.3% 23.89% -9.21% 2.57 PP1a axonemal protein serine/threonine phosphatase 1a 168012 72.02% 28.37% 7.19% 0.77 KAP non-motor subunit of kinesin-II for IFT 155416 76.14% 40.91% 5.6% 1.24 RSP2 radial spoke 2 (spoke stalk, PF24) 157052 76.19% 40.82% -5.26% 0.74 MBO2 mobe2 coiled-coil protein 169254 77.32% 30.59% -5.96% 0.83 IFT88 homolog of Tg737 166736 92.65% 42.85% 3.51% 1.22 IDA7 inner dynein arm I1 intermediate chain IC140 159022 106.16% 35.44% -7.71% 0.83 IFT81 168881 108.69% 73.91% 8.98% 0.8 Tektin Chlamydomonas tektin annotated by Lefebvre 166131 118.52% 43.45% 31.97% 0.97 PF20 central pair microtubule protein 157798 127.93% 33.57% 1% 0.75 ODA3 outer arm docking complex subunit 1 ODA-DC1 156307 133.23% 23.69% 10.76% 0.81 D1bLIC cytoplasmic dynein 1b light intermed chain (retro IFT) 162279 143.86% 56.65% 6.06% 0.95 RSP3 radial spoke 3 (spoke stalk, PF14, AKAP) 164295 159.93% 88.85% 15.33% 1.43 ODA12 outer dynein arm light chain 2 (DLC2 or Tctex2) 171226 164.74% 45.98% -8.08% 1.21 Tctex1 inner arm dynein light chain Tctex1 169383 165.46% 54.52% 26.03% 2.01 IDA4 inner arm dynein light chain p28 154393 168.36% 81.09% 5.86% 1.36 IFT52 BLD1, Osm-6 164100 170.31% 81% 4.73% 0.83 ODA6 outer dynein arm intermediate chain 2 (IC70) 156214 183.92% 37.02% -1.71% 1.31 IFT20 155586 207.12% 129.09% -3.74% 0.6 PF2 dynein regulatory complex component. trypanin related 164979 221.01% 104.7% 30.23% 0.64 IFT74/72 156948 232.55% 56.82% 19% 0.89 IFT57 homology with Hippi (huntingtin interacting protein 1) 171763 239.93% 144.84% -1.09% 0.91 ODA1 outer arm docking complex subunit 2 ODA-DC2 167565 248.19% 90.7% -0.66% 0.75 KLP1 kinesin associated with the central pair 170981 248.61% 81.67% -9.67% 1.49 FAP2 Tctex2-related light chain 169795 251.48% 142.96% 15.57% 3 DLC7a outer arm dynein light chain 7 (Roadblock-like outer arm) 159281 265.12% 128.04% 36.99% 13.83 FLA14 outer dynein arm light chain 8 (LC8) [why is it fla?] 170694 270.91% 119% 0.63% 0.78 RIB43a pf ribbon protein with coiled-coil 171680 289.52% 139.73% 23.18% 1.46 ODA9 outer dynein arm intermediate chain 1 (IC78) 164307 316.27% 133.37% -5.76% 2.18 DLC3 outer dynein arm light chain 3 (16 kDa light chain) 168602 337.65% 246.55% 26.75% 1.11 DLC1 outer dynein arm light chain 1 157968 354.54% 140.72% 5.27% 1.37 RSP6 radial spoke 6 (spoke head, PF26. dimer with pf4) 171096 367.77% 123.03% -4.21% 1.51 PF16 central pair microtubule protein (homolog to Spag6) 168675 377.18% 152.45% 26.45% 1.33 RIB72 pf ribbon protein 157967 382.67% 240.87% 30.47% 1.06 RSP4 radial spoke 4 (spoke head, PF1) 164722 430.58% 330.93% 40.97% 1.45 ODA13 outer dynein arm light chain 6 (11 kDa light chain) 169971 464.3% 333.2% 71.19% 1.4 DLC7b dynein light chain related to Roadblock 160952 676.09% 213.18% 43.84% 1.19 ODA15 outer arm docking complex subunit 3 ODA-DC3 II. B. control genes whose products localize to chloroplast 158611 -57.02% -82.3% -59.07% 15.76 PSBW photosystem II reaction center W protein 160286 -37.96% -51.07% -27.46% 2.4 THYL thylakoid lumenal 17.4 kDa protein 169972 -32.22% -36.25% 6.46% 27.34 PETM cytochrome b6f subunit 165812 -26.4% -45.99% -19.2% 11.02 PETC cytochrome b6f Rieske Iron-sulfur protein 154244 -18.48% -58.55% -36.81% 10.97 PETN cytochrome b6f subunit 156157 -12.17% -43.54% -19.05% 2.07 PGK chloroplast phosphoglycerate kinase 165989 -3.31% -51.55% 5.28% 91.13 RbcS2 Rubisco small subunit 159627 -1.81% -14.54% 8.18% 1.1 CemA chloroplast integral membrane heme-binding protein 154594 4.49% 3.7% 0.16% 0.63 MINE2 MinE chloroplast division protein 169504 4.98% 2.99% 11.25% 0.75 MET1 chloroplast resident DNA methyltransferase II. C. control genes whose products localize to nucleus 162121 -35.64% -41.01% -38.61% 0.93 TAF7 TF IID subunit TAF7 157840 -23.77% -7.05% -6.4% 1.55 HFO1 histone H4 164461 -4.85% -9.7% -4.38% 1.03 NUP98 nucleoporin nup98 163504 -1.62% 8.14% -0.66% 1.53 NUP155 nucleoporin nup155 153542 0.02% -5.65% -5.1% 0.87 RPB1 RNA pol II large subunit 169614 1.44% 8.69% -2.94% 0.69 TOP2 topoisomerase II 170696 5.65% 14.31% -7.34% 0.57 TOP1 topoisomerase I 162123 7.98% -4.2% -5.48% 1.18 POLA2 DNA polymerase alpha subunit B 161483 15.74% -15.66% 23.88% 0.85 TFIIAg TFIIA gamma subunit 152784 21.87% 40.62% 28.9% 0.64 HON1 histone H1 157278 30.77% 1.44% 35.81% 1.03 PCN1 PCNA homolog 164104 91.38% 34.83% 59.42% 0.68 RPB119aa RNA pol II 14.5 kD subunit III. Genes corresponding to potential ciliary diseases 169197 -28.44% -17.24% -15.31% 1.02 DIP13 deflag-inducible protein. Sjogren's syndrome NA 165102 -12.77% -8.36% -3.96% 1.13 PKHD1-1 fibrocystin 164661 -9.43% -4.71% -6.16% 1.06 insulin receptor 168865 -5.95% 2.59% -5.96% 0.58 HIPI1 huntingtin interacting protein 1 156686 -5.53% 9.4% 3.37% 1.03 PKHD1-2 fibrocystin 158670 -4.1% 16.43% 7.14% 0.73 TSLRP zebrafish Seahorse (PKD) testis specific LRR protein 158816 -0.36% -26.73% 16.07% 1.36 NPHP3(?) possible nephrocystin 3 154789 0.55% 1.07% 13.04% 0.95 RP2 retinitis pigmentosa 2 168988 0.69% -1.8% -1.18% 0.79 NPHP3 nephrocystin 3 according to Pazour annotation 156598 1.28% 13.94% -3.15% 0.78 polycystin 1 precursor 154949 1.44% 23.07% -9.97% 1.04 BBS7 163973 2.05% 5% 15.95% 3.39 INVSb inversin isoform b 170819 5.28% -3.29% 20.62% 1.51 SSD3 Niemann-pick related protein in arabidopsis 165845 6% 11.33% -1.34% 0.74 PKHD1-3 fibrocystin (PKD & hepatic disease) 153344 6.42% -18.81% 23.7% 1.64 CFTR atp binding cassette of cftr 168613 8.97% 17.94% -0.65% 0.78 PTCH patched homolog, Niemann-Pick 152526 11.12% 30.17% 2.65% 0.94 BBS1 157801 12.37% 20.52% -15.37% 0.61 OFD1 possible OFD1 (oro-facial_digital syndrome) 159573 17.95% 0% 2.27% 1.16 BBS2 164333 19.68% 5.51% 6.29% 0.95 NPHP4 nephronophthisis (nephroretinin) 152452 19.74% -3.93% 2.63% 0.75 RPGR retinitis pigmentosa GTPase regulator 158679 21.5% 6.62% -14.88% 1.2 ARLB2 possible zebrafish Scorpion homolog (PKD, no cilia) 159460 21.52% 18.99% -11.38% 0.39 G-protein linked with obesity 165004 25.85% 31.32% 5.78% 0.82 Hydin hydrocephalus inducing protein 161738 34.31% 42.88% -15.27% 1.04 BBS5 157469 34.33% 14.93% 7.46% 1 ODA2 human DNAH5 (PCD, situs inversus) 171797 46.3% 12.96% 39.77% 1.07 BBS8 Bardet-Biedl TRP protein 8 157341 56.35% 0.03% 11.53% 1.42 TBY1 Tubby like protein 1 158863 134.99% 49.99% -2.5% 0.8 FAP22 zebrafish QiLin homolog (PKD)