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.


Navigation/Query Panel:
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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2708 to 2757 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1354 NDST3 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Divided 228.409 223.475 1.02208
1355 LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Subtracted 204.961 209.517 4.556
NDST4 n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Divided 228.409 223.475 1.02208
1356 ATF7 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Subtracted 218.667 214.118 4.549
NDST1 heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Divided 228.409 223.475 1.02208
1357 ATF2 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Subtracted 218.657 214.11 4.547
CDC27 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Divided 228.409 223.475 1.02208
1358 PGGT1B geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Subtracted 225.039 229.573 4.534
USF1 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Divided 214.987 210.359 1.022
1359 FADS3 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Subtracted 225.039 229.573 4.534
GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Divided 228.642 223.726 1.02197
1360 SMAD4 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Subtracted 225.039 229.573 4.534
TGFBR1 tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Divided 223.89 228.805 1.02195
1361 FADS2 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] Subtracted 225.039 229.573 4.534
USF2 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Divided 214.971 210.354 1.02195
1362 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Subtracted 225.039 229.573 4.534
PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Divided 228.644 223.736 1.02194
1363 CREB5 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 218.591 213.899
NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Subtracted 168.989 164.46 4.529
1364 ACVR1B serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Divided 223.885 228.797 1.02194
NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Subtracted 168.995 164.467 4.528
1365 ATPIF1 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Divided 228.644 223.736 1.02194
NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Subtracted 169.031 164.507 4.524
1366 ACVR1C activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] Divided 223.884 228.795 1.02194
PRAF2 jm4 protein. [refseq;acc:nm_007213] Subtracted 199.643 204.163 4.52
1367 ARL6IP5 cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] 199.771 204.287 4.516
FREQ neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Divided 223.887 228.799 1.02194
1368 NPC2 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Subtracted 205.204 200.71 4.494
SMOX polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Divided 228.644 223.736 1.02194
1369 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Subtracted 221.152 216.659 4.493
HCCS cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Divided 228.644 223.736 1.02194
1370 CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Subtracted 107.842 112.329 4.487
NCK1 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Divided 205.185 200.784 1.02192
1371 GSTT1 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 228.646 223.744 1.02191
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Subtracted 107.842 112.329 4.487
1372 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 129.913 134.399 4.486
SOCS1 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Divided 216.542 211.908 1.02187
1373 GMFG glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 129.921 134.406 4.485
1374 ASCC2 asc-1 complex subunit p100. [refseq;acc:nm_032204] Divided 216.542 211.908 1.02187
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Subtracted 108.289 112.772 4.483
1375 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
FKBP1A fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Divided 216.542 211.908 1.02187
1376 EYA3 eyes absent homolog 3. [swissprot;acc:q99504] 218.537 213.91 1.02163
RAD23A uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Subtracted 220.987 225.468 4.481
1377 PSMD4 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
SALL2 sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Divided 218.471 213.876 1.02148
1378 OCRL inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Subtracted 220.987 225.468 4.481
SALL3 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Divided 218.47 213.876 1.02148
1379 RAD23B uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Subtracted 220.987 225.468 4.481

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/