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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 730 to 779 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
183 ACADVL Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 79779.8 108084 1.35478
NCBP2 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
NEDD9 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 no value Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 72886.3 98544.5 1.35203
ATG4A 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
OSR1 Ranked odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 237.79 1.15239
SYNCRIP Measured ns1-associated protein 1. [refseq;acc:nm_006372] 4069.83 5252.17 1.29051
185 ADIPOR2 Ranked adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 1.14292
HNRNPR Measured heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 4069.83 5252.17 1.29051
HS3ST6 Squared c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 41502.9 30836.8 1.34589
MAP1LC3B 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 EIF4G1 Measured eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 4071.1 5251.75 1.29001
FLNB 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
HS3ST3A1 Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 41502.9 30836.8 1.34589
MAP1LC3A 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 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 153.548 133.153 1.15317
HS3ST3B1 Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 41502.9 30836.8 1.34589
REV1 Ranked rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 226.582 198.444 1.14179
SNRPD3 Measured small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 4569.48 5885.79 1.28807
188 E2F1 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
HS3ST2 Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 41502.9 30836.8 1.34589
PRMT1 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
STT3B Measured source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 4571.89 5864.86 1.28281
189 DCPS Squared mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 41502.9 30836.8 1.34589
E2F2 Rooted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 46.0352 53.0192 1.15171
PRMT8 Ranked protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 226.582 198.444 1.14179
STT3A Measured oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 4571.89 5864.86 1.28281
190 AQP4 Squared aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 71389.9 96037.6 1.34525
DDOST 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
GABARAP Rooted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 149.165 129.699 1.15009
SNRP70 Ranked u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 226.582 198.444 1.14179
191 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
AQP5 Squared aquaporin 5. [swissprot;acc:p55064] 71388.5 96035.2 1.34525
PLDN Rooted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 63.1192 72.584 1.14995
SF3B1 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
192 AQP2 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
ARAF 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
MSI2 Ranked musashi 2 isoform a. [refseq;acc:nm_138962] 227.491 199.458 1.14055
SF4 Rooted splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 53.6107 61.5862 1.14877
193 MIP Squared lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 71386.9 96032.5 1.34524
MSI1 Ranked musashi 1. [refseq;acc:nm_002442] 227.491 199.458 1.14055
NOSTRIN Rooted nostrin. [refseq;acc:nm_052946] 59.6399 51.9242 1.1486
RAF1 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
194 AQP1 Squared aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 71346.6 95965.1 1.34505
CCNG2 Measured cyclin g2. [swissprot;acc:q16589] 17738.6 13995.7 1.26743
SNF8 Rooted eap30 subunit of ell complex. [refseq;acc:nm_007241] 59.6399 51.9242 1.1486
ZC3H14 Ranked nuclear protein ukp68. [refseq;acc:nm_024824] 227.491 199.458 1.14055
195 CCNG1 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 13995.6 1.26743
PRPF40B Ranked huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 200.417 1.13748
SLC39A6 Rooted liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 59.6399 51.9242 1.1486

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
- Hugo is the HGNC identifier if it exists
- 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/