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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Network Comparison Type Gene Value Type description Rank network_comparison Filtered Interaction Map red green
Results: HTML CSV LaTeX Showing element 3051 to 3100 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
red
green
ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670] 2729 1.00031 202.123 202.06
ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] 2681 1.00096 203.592 203.787
ubiquitin. [swissprot;acc:p02248] 1148 1.02724 209.061 203.518
1190 1.02558 209.6 204.372
2310 1.00505 216.617 215.529
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] 2333 1.00452 229.258 230.294
udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] 2810 1 0.00001 0.00001
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 1338 1.02257 215.162 210.412
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] 2299 1.00511 215.239 216.339
udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224] 2835 1 0.00001 0.00001
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 3085
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 2819
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 3086
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 2793
udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [swissprot;acc:q9by64] 2979
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 2889
udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662] 2818
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] 1265 1.02425 171.231 167.177
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] 2401 1.00374 182.4 183.083
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 345 1.09729 242.14 265.697
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] 2522 1.00234 215.835 216.341
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 3030 1 0.00001 0.00001
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 29 1.29991 187.458 243.678
unr protein. [swissprot;acc:o75534] 828 1.0431 230.087 220.579
upf0183 protein. [swissprot;acc:q9bsu1] 2417 1.00359 218.2 218.984
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 760 1.04946 246.055 234.458
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 1191 1.02558 220.742 215.237
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] 1358 1.022 214.987 210.359
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] 1361 1.02195 214.971 210.354
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 1220 1.025 211.959 217.258
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] 755 1.04968 224.434 235.583
uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533] 2772 1 0.00001 0.00001
uridine kinase-like 1. [swissprot;acc:q9nwz5] 1502 1.01838 218.084 214.149
uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132] 3010 1 0.00001 0.00001
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 1609 1.0158 208.113 204.876
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] 2580 1.00154 213.422 213.75
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] 1431 1.02028 220.987 225.468
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] 1434
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] 1311 1.02341 226.439 221.26
vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384] 3136 1 0.00001 0.00001
vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296] 3204
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 1175 1.02593 218.186 212.672
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] 1180
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] 1056 1.03079 219.01 212.468
vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787] 2782 1 0.00001 0.00001
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 1135 1.02731 218.484 212.675
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] 1146 1.0273 218.483 212.676
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] 1142 1.02731 218.484 212.675
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] 1187 1.02582 218.402 212.904
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] 1138 1.02731 218.484 212.675

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/