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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 725 to 774 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
182 Measured rna-binding protein. [refseq;acc:nm_019027] 4069.83 5252.17 1.29051
Ranked histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 277.546 240.461 1.15422
Squared deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 61733.5 45224.1 1.36506
Rooted t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 57.45 66.332 1.1546
183 Measured apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 4069.83 5252.17 1.29051
Ranked 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 228.306 198.011 1.153
Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 79779.8 108084 1.35478
Rooted enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 57.4586 66.3336 1.15446
184 Measured ns1-associated protein 1. [refseq;acc:nm_006372] 4069.83 5252.17 1.29051
Ranked odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 237.79 1.15239
Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 72886.3 98544.5 1.35203
Rooted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 153.602 133.195 1.15321
185 Measured heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 4069.83 5252.17 1.29051
Ranked adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 1.14292
Squared c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 41502.9 30836.8 1.34589
Rooted microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 153.578 133.176 1.1532
186 Measured eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 4071.1 5251.75 1.29001
Ranked filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 226.582 198.444 1.14179
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 41502.9 30836.8 1.34589
Rooted microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 153.578 133.176 1.1532
187 Measured small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 4569.48 5885.79 1.28807
Ranked rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 226.582 198.444 1.14179
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 41502.9 30836.8 1.34589
Rooted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 153.548 133.153 1.15317
188 Measured source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 4571.89 5864.86 1.28281
Ranked protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 226.582 198.444 1.14179
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 41502.9 30836.8 1.34589
Rooted 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] 46.0352 53.0192 1.15171
189 Measured oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 4571.89 5864.86 1.28281
Ranked protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 226.582 198.444 1.14179
Squared mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 41502.9 30836.8 1.34589
Rooted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 46.0352 53.0192 1.15171
190 Measured dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 4571.89 5864.86 1.28281
Ranked u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 226.582 198.444 1.14179
Squared aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 71389.9 96037.6 1.34525
Rooted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 149.165 129.699 1.15009
191 Measured splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 4638.1 5923.4 1.27712
Ranked filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 226.582 198.444 1.14179
Squared aquaporin 5. [swissprot;acc:p55064] 71388.5 96035.2 1.34525
Rooted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 63.1192 72.584 1.14995
192 Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 14008 1.26767
Ranked musashi 2 isoform a. [refseq;acc:nm_138962] 227.491 199.458 1.14055
Squared aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 71387.4 96033.4 1.34524
Rooted splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 53.6107 61.5862 1.14877
193 Measured raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 17756.5 14007.3 1.26766
Ranked musashi 1. [refseq;acc:nm_002442] 227.491 199.458 1.14055
Squared lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 71386.9 96032.5 1.34524
Rooted nostrin. [refseq;acc:nm_052946] 59.6399 51.9242 1.1486
194 Measured cyclin g2. [swissprot;acc:q16589] 17738.6 13995.7 1.26743
Ranked nuclear protein ukp68. [refseq;acc:nm_024824] 227.491 199.458 1.14055

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/