Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 575 to 624 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
288 blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Low confidence 8155.32 8641.69 1.05964
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] High confidence 23422.4 19380.3 1.20857
289 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Low confidence 7752.95 8214.32 1.05951
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] High confidence 4682.88 5646.19 1.20571
290 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Low confidence 6885.52 7293.37 1.05923
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] High confidence 4991.48 6014.08 1.20487
291 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 36927.5 1.20481
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Low confidence 6885.52 7293.37 1.05923
292 60s ribosomal protein l27. [swissprot;acc:p08526] 7860.4 8325.71 1.0592
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence 4641.09 5588.75 1.20419
293 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence 7675.19 8129.16 1.05915
294 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] High confidence 22515.5 18702.6 1.20387
ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] Low confidence 7590.39 8039.23 1.05913
295 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 9113.16 9650.42 1.05895
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] High confidence 13261.9 11017.8 1.20368
296 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 4911.81 5909.18 1.20306
tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Low confidence 8417.28 8911.22 1.05868
297 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] 8414.05 8907.06 1.05859
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] High confidence 4911.81 5909.18 1.20306
298 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Low confidence 8708.47 9218.39 1.05855
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] High confidence 4633.92 5572.85 1.20262
299 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Low confidence 8904.93 9426.29 1.05855
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] High confidence 4914.27 5907.12 1.20203
300 nitrogen fixation cluster-like. [refseq;acc:nm_014301] Low confidence 8667.67 9173.88 1.0584
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] High confidence 4914.27 5907.12 1.20203
301 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 13768.2 11466 1.20078
epsin 3. [refseq;acc:nm_017957] Low confidence 8559.94 9059.13 1.05832
302 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] High confidence 5894.75 7073.65 1.19999
tfiih basal transcription factor complex p34 subunit (basic transcription factor 2 34 kda subunit) (btf2-p34) (general transcription factor iih polypeptide 3). [swissprot;acc:q13889] Low confidence 9243.98 9781.77 1.05818
303 homeobox protein nkx-6.1. [swissprot;acc:p78426] 9810.95 10381.3 1.05813
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] High confidence 22268.8 18560.4 1.1998
304 nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] Low confidence 9810.95 10381.3 1.05813
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 4855.46 5824.52 1.19958
305 cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] Low confidence 9810.95 10381.3 1.05813
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] High confidence 3856.29 4624.15 1.19912
306 pnas-18. [sptrembl;acc:q9bzu3] 13680.5 11409.6 1.19903
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Low confidence 7941.76 8403.21 1.0581
307 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 7943.99 8405.13 1.05805
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] High confidence 12365.2 14824.9 1.19892
308 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Low confidence 7944.21 8405.32 1.05804
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] High confidence 4977.09 5966.44 1.19878
309 ras-related protein rab-26. [swissprot;acc:q9ulw5] Low confidence 10765.1 10174.7 1.05803
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] High confidence 4977.8 5966.14 1.19855
310 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Low confidence 7945.12 8406.1 1.05802
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] High confidence 4909.79 5878.79 1.19736
311 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Low confidence 7398.26 7826.48 1.05788
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] High confidence 4981.52 5964.58 1.19734
312 coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] Low confidence 7696.96 8141.6 1.05777
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] High confidence 4598.21 5500.48 1.19622

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/