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 633 to 682 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
317 adiponectin receptor 2. [refseq;acc:nm_024551] Divided 3153.1 3762.56 1.19329
vav-3 protein. [swissprot;acc:q9ukw4] Subtracted 6647.43 7706.18 1058.75
318 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 7485.08 8543.66 1058.58
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 34190.9 40795.8 1.19318
319 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Subtracted 7477 8532.02 1055.02
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Divided 20911 24908.5 1.19117
320 ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Subtracted 10263.8 11318.6 1054.8
321 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Divided 20911 24908.5 1.19117
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Subtracted 11797.1 10750.2 1046.9
322 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Divided 20911 24908.5 1.19117
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Subtracted 9304.83 10347.3 1042.47
323 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] 10247.8 11289 1041.2
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 4620.76 5501.94 1.1907
324 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 28136.5 33457.6 1.18912
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Subtracted 11773.7 10733.8 1039.9
325 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 8362.81 9402.7 1039.89
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Divided 16177.9 19235.4 1.18899
326 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 3432.96 4081.21 1.18883
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Subtracted 11773 10733.2 1039.8
327 peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284]
septin 10 isoform 1. [refseq;acc:nm_144710] Divided 16067.4 19094.4 1.18839
328 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 1.18801
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Subtracted 11773 10733.2 1039.8
329 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Divided 15999.1 19007.1 1.18801
330 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Subtracted 11773 10733.2 1039.8
septin 6. [swissprot;acc:q14141] Divided 15959.9 18957.1 1.1878
331 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Subtracted 10246.1 11285.8 1039.7
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Divided 20287.2 17083.8 1.18751
332 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 5051.16 5975.51 1.183
vav-2 protein. [swissprot;acc:p52735] Subtracted 6660.02 7697.78 1037.76
333 deltex 2. [refseq;acc:nm_020892] 1618.84 2651.88 1033.04
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Divided 5039.63 5961.83 1.18299
334 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Subtracted 1629.21 2662.12 1032.91
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Divided 14924.4 17655.2 1.18298
335 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Subtracted 1631.67 2664.55 1032.88
336 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 3751.3 4431.34 1.18128
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted 1631.67 2664.55 1032.88
337 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 20446.1 24136.4 1.18049
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Subtracted 1631.67 2664.55 1032.88
338 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 20446.1 24136.4 1.18049
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Subtracted 1631.67 2664.55 1032.88
339 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided 20446.1 24136.4 1.18049
neuralized-like. [refseq;acc:nm_004210] Subtracted 1657.68 2690.25 1032.57
340 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 20446.1 24136.4 1.18049
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Subtracted 11743.3 10712.3 1031
341 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 20446.1 24136.4 1.18049
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted 4916.8 3888.18 1028.62

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/