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 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
description
Interaction Map
red
green
network_comparison
313 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Low confidence 202.05 193.94 1.04182
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 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 1.10027
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 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
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 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 209.583 201.251 1.0414
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] High confidence 242.694 267.017 1.10022
317 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
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
318 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 266.18 1.09987
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Low confidence 209.579 201.251 1.04138
319 60s ribosomal protein l19. [swissprot;acc:p14118] High confidence 240.73 264.729 1.09969
heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082] Low confidence 212.752 204.328 1.04123
320 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] High confidence 241.892 265.96 1.0995
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 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
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Low confidence 207.402 199.219 1.04108
322 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] 212.262 203.991 1.04055
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] High confidence 86.7483 78.8995 1.09948
323 60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 265.945 1.09947
integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] Low confidence 212.262 203.991 1.04055
324 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 243.944 268.195 1.09941
rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] Low confidence 212.262 203.991 1.04055
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] High confidence 243.944 268.195 1.09941
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Low confidence 199.905 192.123 1.04051
326 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 241.899 265.924 1.09932
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] Low confidence 199.343 191.59 1.04047
327 bet3 homolog. [swissprot;acc:o43617] 197.221 189.574 1.04034
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] High confidence 243.817 267.962 1.09903
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 1.09888
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 exocyst complex component exo70. [swissprot;acc:q9upt5] 204.124 212.339 1.04025
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 312 284 1.09859
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 221.437 212.889 1.04015
331 doc-1 related protein (doc-1r). [swissprot;acc:o75956] High confidence 312 284 1.09859
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 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 209.495 201.474 1.03981
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 312 284 1.09859
333 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Low confidence 200.482 208.446 1.03972
334 coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] 202.616 194.878 1.03971
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 312 284 1.09859
335 bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Low confidence 202.616 194.878 1.03971
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence 312 284 1.09859
336 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]
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Low confidence 202.616 194.878 1.03971
337 60s ribosomal protein l12. [swissprot;acc:p30050] High confidence 243.583 267.527 1.0983
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
- 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/