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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 description Gene Network Comparison Type Hugo Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1247 to 1296 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Hugo
Interaction Map
red
green
network_comparison
312 transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Subtracted BACH1 Low confidence 172.647 164.44 8.207
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Divided SNRPA1 202.051 193.937 1.04184
313 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value 202.05 193.94 1.04182
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted MAGEA9 High confidence 88.2482 110.265 22.0168
nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 Low confidence 172.647 164.44 8.207
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Divided RRM2B High confidence 232.473 211.207 1.10069
314 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted MAGEA8 88.2482 110.265 22.0168
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Divided METAP1 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] SF3B1 Low confidence 202.057 193.952 1.04179
transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Subtracted BACH2 172.647 164.44 8.207
315 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] SNORD23 207.402 199.219 8.183
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 High confidence 88.2482 110.265 22.0168
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] Divided METAP2 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] TNKS Low confidence 214.067 205.509 1.04164
316 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted MAGEA4 High confidence 88.2482 110.265 22.0168
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Divided KCNA2 Low confidence 209.583 201.251 1.0414
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] EIF1 High confidence 242.694 267.017 1.10022
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Subtracted SNRPA1 Low confidence 202.051 193.937 8.114
317 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value High confidence 88.2482 110.265 22.0168
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Low confidence 200.213 192.103 8.11
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Divided KCNA1 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] no value High confidence 224.445 204.044 1.09998
318 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Subtracted Low confidence 202.05 193.94 8.11
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 88.2482 110.265 22.0168
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Divided MRPL3 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] KCNA4 Low confidence 209.579 201.251 1.04138
319 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 High confidence 240.73 264.729 1.09969
heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082] HSPB2 Low confidence 212.752 204.328 1.04123
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted MAGEB4 High confidence 88.2482 110.265 22.0168
mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] MRPL44 Low confidence 216.283 208.173 8.11
320 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Divided CDH1 High confidence 241.892 265.96 1.0995
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted MAGED2 88.2482 110.265 22.0168
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] Divided PHKG2 Low confidence 217.756 226.722 1.04117
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted SF3B1 202.057 193.952 8.105
321 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Divided no value High confidence 241.892 265.959 1.09949
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted DYNC1I1 Low confidence 209.495 201.474 8.021
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Divided SNORD23 207.402 199.219 1.04108
trophinin. [swissprot;acc:q12816] Subtracted TRO High confidence 88.2482 110.265 22.0168
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] Divided NUDT21 Low confidence 212.262 203.991 1.04055
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B High confidence 86.7483 78.8995 1.09948
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Subtracted GGPS1 Low confidence 209.518 201.554 7.964
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 High confidence 231.969 210.064 21.905
323 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] RPS14 242.238 264.11 21.872
60s ribosomal protein l23a. [swissprot;acc:p29316] Divided no value 241.884 265.945 1.09947
integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] ITGB1BP2 Low confidence 212.262 203.991 1.04055
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Subtracted C20orf43 200.482 208.446 7.964
324 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] no value High confidence 242.238 264.11 21.872
40s ribosomal protein s23. [swissprot;acc:p39028] Divided RPS23 243.944 268.195 1.09941
rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] RAB3GAP2 Low confidence 212.262 203.991 1.04055
spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Subtracted SPSB4 219.655 211.763 7.892

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/