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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1258 to 1307 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
315 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Subtracted 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] METAP2 Divided 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] MAGEA4 Subtracted 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] KCNA2 Divided 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] SNRPA1 Subtracted 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] KCNA1 Divided 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] MRPL3 Divided 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] MAGEB4 Subtracted 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] CDH1 Divided 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] MAGED2 Subtracted 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] PHKG2 Divided 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] SF3B1 Subtracted 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] no value Divided High confidence 241.892 265.959 1.09949
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] DYNC1I1 Subtracted Low confidence 209.495 201.474 8.021
glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] SNORD23 Divided 207.402 199.219 1.04108
trophinin. [swissprot;acc:q12816] TRO Subtracted 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] NUDT21 Divided 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] GGPS1 Subtracted 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] no value Divided 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] C20orf43 Subtracted 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] RPS23 Divided 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] SPSB4 Subtracted 219.655 211.763 7.892
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] MRPS12 Divided High confidence 243.944 268.195 1.09941
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] MRPL13 Subtracted 241.828 263.62 21.792
fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] AFF2 Low confidence 219.599 211.723 7.876
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Divided 199.905 192.123 1.04051
326 40s ribosomal protein s16. [swissprot;acc:p17008] RPS16 Subtracted High confidence 241.828 263.62 21.792
60s ribosomal protein l5. [swissprot;acc:p46777] RPL5 Divided 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] DDOST Low confidence 199.343 191.59 1.04047
laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] AFF3 Subtracted 219.598 211.722 7.876
327 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] RPL13A High confidence 241.83 263.615 21.785
all1 fused gene from 5q31. [refseq;acc:nm_014423] AFF4 Low confidence 219.598 211.722 7.876
bet3 homolog. [swissprot;acc:o43617] TRAPPC3 Divided 197.221 189.574 1.04034

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/