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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2025 to 2074 of 8289 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
1013 HEATR1 protein bap28. [swissprot;acc:q9h583] High confidence 244.312 236.647 1.03239
IMPDH2 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Low confidence 200.743 195.959 1.02441
1014 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] High confidence 243.045 235.422 1.03238
MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence 182.56 178.211 1.0244
1015 KIFC3 kinesin family member c3. [refseq;acc:nm_005550] 205.25 200.362
MAGI1 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] High confidence 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
TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Low confidence 201.283 196.49 1.02439
1017 IMPDH1 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] 200.745 195.966
TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] High confidence 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
PDZRN3 similar to semaf cytoplasmic domain associated protein 3. [sptrembl;acc:q96cc2] Low confidence 204.339 199.475 1.02438
1019 HIPK3 homeodomain interacting protein kinase 3; homeodomain-interacting protein kinase 3. [refseq;acc:nm_005734] 202.352 197.536
TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] High confidence 221.302 214.409 1.03215
1020 DCT dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] 221.28 1.03205
TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Low confidence 200.421 205.306 1.02437
1021 HIPK2 homeodomain-interacting protein kinase 2 (ec 2.7.1.-). [swissprot;acc:q9h2x6] 202.351 197.537
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] High confidence 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
HIPK1 homeodomain-interacting protein kinase 1; homeodomain interacting protein kinase 1-like protein; nuclear body associated kinase 2b. [refseq;acc:nm_152696] Low confidence 202.351 197.538 1.02436
1023 RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] High confidence 205.632 199.266 1.03195
UNC50 geal-6 membrane-associated high-copy suppressor 1; unc-50 related. [refseq;acc:nm_014044] Low confidence 203.215 208.165 1.02436
1024 TIMM9 mitochondrial import inner membrane translocase subunit tim9 a. [swissprot;acc:q9y5j7] 205.995 201.097
TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] High confidence 205.632 199.266 1.03195
1025 MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
NAP1L2 nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6] Low confidence 201.047 196.275 1.02431
1026 RHOA transforming protein rhoa (h12). [swissprot;acc:p06749] High confidence 205.632 199.266 1.03195
SGCG gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Low confidence 206.781 201.874 1.02431
1027 PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] 203.643 198.811 1.0243
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] High confidence 211.908 218.627 1.03171
1028 SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Low confidence 203.574 198.744 1.0243
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] High confidence 211.908 218.627 1.03171
1029 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 1.03168
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Low confidence 204.847 199.989 1.02429
1030 no value nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 201.043 196.276
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] High confidence 222.364 215.535 1.03168
1031 EMG1 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 242.978 235.518 1.03167
TBXAS1 thromboxane-a synthase (ec 5.3.99.5) (txa synthase) (txs). [swissprot;acc:p24557] Low confidence 203.998 199.161 1.02429
1032 AGPAT2 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] High confidence 186.664 180.943 1.03162
SH3GL1 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Low confidence 203.946 199.111 1.02428
1033 SEPT4 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] 172.447 168.363 1.02426
TYR tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] High confidence 221.183 214.406 1.03161
1034 no value multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Low confidence 202.723 197.922 1.02426
ESRRB steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] High confidence 186.551 180.837 1.0316
1035 MAGI2 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 221.682 228.68 1.03157
NAP1L1 nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209] Low confidence 201.037 196.277 1.02425
1036 COPB1 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] High confidence 171.341 176.746 1.03155
RAB7A ras-related protein rab-7. [swissprot;acc:p51149] Low confidence 199.336 194.616 1.02425
1037 GLRX3 thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] High confidence 228.412 235.609 1.03151
PSPHL l-3-phosphoserine phosphatase (ec 3.1.3.3) (psp) (o-phosphoserine phosphohydrolase) (pspase). [swissprot;acc:p78330] Low confidence 195.067 190.451 1.02424

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/