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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1001 DCT dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Subtracted 221.28 214.409 6.871
SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Divided 225.167 217.922 1.03325
1002 SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
TYRP1 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Subtracted 221.278 214.409 6.869
1003 PNN pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 211.071 204.205 6.866
SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Divided 225.167 217.922 1.03325
1004 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 231.059 1.03318
FHL3 skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Subtracted 269.59 276.454 6.864
1005 DKC1 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 231.007 237.864 6.857
DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Divided 225.448 218.232 1.03307
1006 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 116.524 120.375 1.03305
RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Subtracted 217.026 210.189 6.837
1007 RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Divided 162.055 156.884 1.03296
RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Subtracted 217.021 210.185 6.836
1008 DDB1 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 222.364 215.535 6.829
WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] Divided 243.227 235.475 1.03292
1009 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 229.116 221.823 1.03288
PCCB propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Subtracted 222.364 215.535 6.829
1010 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 228.105 221.293 6.812
CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Divided 217.523 210.648 1.03264
1011 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted 228.105 221.293 6.812
RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Divided 217.026 210.189 1.03253
1012 KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Subtracted 217.369 210.561 6.808
RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Divided 217.021 210.185 1.03252
1013 HEATR1 protein bap28. [swissprot;acc:q9h583] 244.312 236.647 1.03239
TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Subtracted 217.365 210.558 6.807
1014 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Divided 243.045 235.422 1.03238
KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Subtracted 217.361 210.554 6.807
1015 EXOC3 exocyst complex component sec6. [swissprot;acc:o60645] 207.186 200.398 6.788
MAGI1 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Divided 221.73 228.906 1.03236
1016 KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 217.369 210.561 1.03233
TYR tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Subtracted 221.183 214.406 6.777
1017 SUCLG1 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] 211.908 218.627 6.719
TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided 217.365 210.558 1.03233
1018 KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 210.554
SUCLA2 succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] Subtracted 211.908 218.627 6.719
1019 no value 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 6.695
TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 221.302 214.409 1.03215
1020 no value similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 226.218 232.88 6.662
DCT dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Divided 221.28 214.409 1.03205
1021 no value block 23. [sptrembl;acc:q8nhw5] Subtracted 226.205 232.858 6.653
TYRP1 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Divided 221.278 214.409 1.03204
1022 CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 205.632 199.266 1.03195
RPLP0 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Subtracted 226.203 232.855 6.652
1023 BLOC1S1 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 202.027 195.386 6.641
RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Divided 205.632 199.266 1.03195
1024 DPM1 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Subtracted 203.381 196.76 6.621
TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Divided 205.632 199.266 1.03195
1025 FAU 40s ribosomal protein s30. [swissprot;acc:q05472] Subtracted 223.44 216.875 6.565
MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Divided 205.632 199.266 1.03195

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/