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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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 6914 to 6963 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
865 no value alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Squared Subtracted 26583.7 30425.2 3841.5
ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Rooted Divided 62.7551 66.6474 1.06202
BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Ranked 211.961 203.814 1.03997
CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Rooted Subtracted 62.2332 58.3925 3.8407
PIK3R1 phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Measured Divided 5595.65 6173.23 1.10322
SCAP sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Squared 24242.8 28127.6 1.16025
ZNF174 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Ranked Subtracted 269.963 278.239 8.276
866 no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 269.96 278.232 8.272
ATP5B atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Squared Divided 24242.8 28127.6 1.16025
EMG1 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Rooted 51.8306 55.0247 1.06163
ESD esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Squared Subtracted 26583.7 30425.2 3841.5
NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Measured 4510.61 5098.74 588.13
RNF38 ring finger protein 38. [refseq;acc:nm_022781] Divided 5595.65 6173.23 1.10322
SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Ranked 221.306 212.806 1.03994
TRIP10 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Rooted Subtracted 62.5007 58.6648 3.8359
867 no value 40s ribosomal protein s3a. [swissprot;acc:p49241] Ranked Divided 225.689 234.674 1.03981
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Squared Subtracted 19263.3 23092.3 3829
MAD2L2 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Rooted Divided 61.668 65.4526 1.06137
PIK3R2 phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Squared 24242.8 28127.6 1.16025
PIK3R3 phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Measured 5595.65 6173.23 1.10322
RAB3IL1 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Subtracted 6545.19 7132.89 587.7
RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Rooted 64.1165 67.9451 3.8286
ZNF18 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Ranked 269.956 278.223 8.267
868 no value keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Squared Divided 31099.4 36082.4 1.16023
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Rooted 61.668 65.4526 1.06137
HLCS biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Measured Subtracted 5607.43 6194.98 587.55
MVD diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Ranked Divided 233.298 242.571 1.03975
RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Rooted Subtracted 64.1184 67.9467 3.8283
SCAP sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Measured Divided 5595.65 6173.23 1.10322
STX6 syntaxin 6. [swissprot;acc:o43752] Squared Subtracted 26720.4 30548.3 3827.9
ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Ranked 269.956 278.223 8.267
869 ATP5B atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Measured Divided 5595.65 6173.23 1.10322
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Squared 20273.1 23521.2 1.16022
EXOC4 exocyst complex component sec8. [swissprot;acc:q96a65] Ranked 217.762 209.449 1.03969
NUP88 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Rooted 61.668 65.4526 1.06137
PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Subtracted 100.26 96.4491 3.8109
RAB3IP rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Measured 6540.61 7127.41 586.8
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Squared 26702.8 30522.5 3819.7
ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Ranked 269.955 278.221 8.266
870 no value dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Squared 24856.2 28661.3 3805.1
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Divided 21086.3 24464.1 1.16019
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Ranked 211.908 203.832 1.03962
AGXT serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Measured Subtracted 6390.28 6973.08 582.8
MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Rooted Divided 84.6378 89.8201 1.06123
PIK3R2 phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Measured 5595.65 6173.23 1.10322
WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Rooted Subtracted 60.6929 64.4864 3.7935
ZSCAN12 zinc finger protein 305. [swissprot;acc:o43309] Ranked 269.954 278.219 8.265
871 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 110.2 114.552 1.03949
DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Measured Subtracted 3849.94 4431.36 581.42
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Squared Divided 20281 23528.5 1.16013

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/