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 2351 to 2400 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
294 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted High confidence 59.0296 65.951 1.11725
ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] Measured Low confidence 7590.39 8039.23 1.05913
295 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Squared High confidence 30807.7 39351.7 1.27733
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Measured Low confidence 9113.16 9650.42 1.05895
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked High confidence 223.273 202.423 1.103
myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence 218.713 209.709 1.04294
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured High confidence 13261.9 11017.8 1.20368
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 59.029 65.9421 1.11711
tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] Low confidence 66.6351 70.2333 1.054
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Squared 57470.4 53017.7 1.08399
296 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Rooted High confidence 63.0663 56.4667 1.11688
fibulin-1 precursor. [swissprot;acc:p23142] Squared Low confidence 51225 47264.3 1.0838
jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Ranked 218.714 209.709 1.04294
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] High confidence 241.282 266.12 1.10294
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Rooted Low confidence 84.7416 89.3094 1.0539
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured High confidence 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
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared High confidence 28878.8 36783.5 1.27372
297 60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 235.727 259.984 1.1029
fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] Measured Low confidence 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
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Squared Low confidence 48958.6 45174.5 1.08377
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Ranked 218.714 209.709 1.04294
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 61.3254 58.1927 1.05383
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Squared High confidence 14247.4 18142.1 1.27336
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Rooted 63.0663 56.4667 1.11688
298 bet3 homolog. [swissprot;acc:o43617] Low confidence 75.2506 79.2999 1.05381
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Ranked High confidence 268.632 243.588 1.10281
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Measured Low confidence 8708.47 9218.39 1.05855
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Ranked 218.715 209.71 1.04294
n-acetylglutamate synthase. [refseq;acc:nm_153006] Squared 55642.1 60278.3 1.08332
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] High confidence 14247.4 18142.1 1.27336
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] Rooted 57.6823 64.4212 1.11683
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 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
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Ranked 268.635 243.592 1.10281
endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3] Low confidence 208.915 200.322 1.0429
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Squared 51585.2 47618.4 1.0833
heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082] Rooted 68.172 71.8299 1.05366
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared High confidence 28896.2 36767 1.27238
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 59.026 65.8955 1.11638
300 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Ranked Low confidence 218.661 209.669 1.04289
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 150.959 166.351 1.10196
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Rooted 48.1584 53.7378 1.11586
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured Low confidence 8667.67 9173.88 1.0584
plasma membrane calcium-transporting atpase 3 (ec 3.6.3.8) (pmca3) (plasma membrane calcium pump isoform 3) (plasma membrane calcium atpase isoform 3). [swissprot;acc:q16720] Squared 49511.1 45712.9 1.08309
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Rooted 70.2592 74.0161 1.05347
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared High confidence 28896.2 36767 1.27238
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Measured 4914.27 5907.12 1.20203

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/