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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 601 to 650 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
301 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Divided 13768.2 11466 1.20078
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 4446.72 5553.79 1107.07
302 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 5894.75 7073.65 1.19999
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted 6704.44 7811.45 1107.01
303 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 22268.8 18560.4 1.1998
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 4723.53 5828.46 1104.93
304 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1093.07
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 4855.46 5824.52 1.19958
305 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
paxillin. [swissprot;acc:p49023] Subtracted 5221.28 6314.35 1093.07
306 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 8430.03 9518.11 1088.08
pnas-18. [sptrembl;acc:q9bzu3] Divided 13680.5 11409.6 1.19903
307 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Subtracted 7556.75 8636.87 1080.12
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 12365.2 14824.9 1.19892
308 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Subtracted 11852.9 10773.5 1079.4
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Divided 4977.09 5966.44 1.19878
309 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Subtracted 11848.8 10770.3 1078.5
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided 4977.8 5966.14 1.19855
310 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] Subtracted 7551.8 8630.06 1078.26
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] Divided 4909.79 5878.79 1.19736
311 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Subtracted 2820.51 3897.1 1076.59
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 4981.52 5964.58 1.19734
312 max protein. [swissprot;acc:p25912] Subtracted 4640.26 5704.87 1064.61
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Divided 4598.21 5500.48 1.19622
313 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 21644.2 18098.7 1.1959
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Subtracted 4567.04 5631.2 1064.16
314 ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 6563.65 7627.29 1063.64
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Divided 21632.5 18090 1.19583
315 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 21370.8 17896.5 1.19413
vav proto-oncogene. [swissprot;acc:p15498] Subtracted 6644.99 7707.8 1062.81
316 serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided 21370.8 17896.5 1.19413
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 6603.41 7664.65 1061.24
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

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/