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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 625 to 674 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
313 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Low confidence 202.05 193.94 1.04182
RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] High confidence 232.473 211.207 1.10069
314 METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 1.10027
SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Low confidence 202.057 193.952 1.04179
315 METAP2 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] High confidence 244.126 268.604 1.10027
TNKS tankyrase 1 (ec 2.4.2.30) (tank1) (tankyrase i) (tnks-1) (trf1- interacting ankyrin-related adp-ribose polymerase). [swissprot;acc:o95271] Low confidence 214.067 205.509 1.04164
316 EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] High confidence 242.694 267.017 1.10022
KCNA2 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Low confidence 209.583 201.251 1.0414
317 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] High confidence 224.445 204.044 1.09998
KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Low confidence 209.58 201.251 1.04139
318 KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 209.579 1.04138
MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] High confidence 242.011 266.18 1.09987
319 HSPB2 heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082] Low confidence 212.752 204.328 1.04123
RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] High confidence 240.73 264.729 1.09969
320 CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 241.892 265.96 1.0995
PHKG2 phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] Low confidence 217.756 226.722 1.04117
321 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] High confidence 241.892 265.959 1.09949
SNORD23 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Low confidence 207.402 199.219 1.04108
322 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] High confidence 86.7483 78.8995 1.09948
NUDT21 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Low confidence 212.262 203.991 1.04055
323 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] High confidence 241.884 265.945 1.09947
ITGB1BP2 integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] Low confidence 212.262 203.991 1.04055
324 RAB3GAP2 rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414]
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 243.944 268.195 1.09941
325 MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Low confidence 199.905 192.123 1.04051
326 DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 199.343 191.59 1.04047
RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 241.899 265.924 1.09932
327 POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 243.817 267.962 1.09903
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Low confidence 197.221 189.574 1.04034
328 DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] High confidence 258.437 235.183 1.09888
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence 203.162 195.289 1.04031
329 EXOC7 exocyst complex component exo70. [swissprot;acc:q9upt5] 204.124 212.339 1.04025
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 312 284 1.09859
330 CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
RGN senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 221.437 212.889 1.04015
331 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] High confidence 312 284 1.09859
GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 200.249 192.535 1.04007
332 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 209.495 201.474 1.03981
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 312 284 1.09859
333 C20orf43 protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Low confidence 200.482 208.446 1.03972
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] High confidence 312 284 1.09859
334 BICD2 coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] Low confidence 202.616 194.878 1.03971
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 312 284 1.09859
335 BICD1 bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Low confidence 202.616 194.878 1.03971
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence 312 284 1.09859
336 CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Low confidence 202.616 194.878 1.03971
337 no value 60s ribosomal protein l12. [swissprot;acc:p30050] High confidence 243.583 267.527 1.0983
CDKL1 serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Low confidence 201.873 194.181 1.03961

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/