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 1060 to 1109 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
265 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided 1 225.217 202.459 1.11241
266 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 0 5813.32 6706.32 893
ribosomal protein l10-like protein. [refseq;acc:nm_080746] 1 243.12 266.662 23.542
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Divided 0 13483.3 14685.4 1.08915
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 1 241.07 267.88 1.11121
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 243.12 266.661 23.541
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 10783 11674.1 891.1
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Divided 1 241.07 267.88 1.11121
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 0 8054.34 8772.02 1.0891
268 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Subtracted 10438.3 9549.77 888.53
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Divided 1 271.016 244.167 1.10996
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 0 14257.4 13134.5 1.08549
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 1 241.625 265.136 23.511
269 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Divided 241.373 267.352 1.10763
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 12463.5 11482.6 1.08542
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Subtracted 8907.41 9795.36 887.95
270 40s ribosomal protein s3. [swissprot;acc:p23396] 1 241.612 265.119 23.507
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 0 11644 10763.4 880.6
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Divided 10735.1 9891.37 1.0853
fad synthetase. [refseq;acc:nm_025207] 1 241.373 267.352 1.10763
271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 0 5781.93 6660.63 878.7
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Divided 10735.1 9891.37 1.0853
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 1 243.072 266.559 23.487
272 fos-related antigen 2. [swissprot;acc:p15408] 0 7091.75 6217.28 874.47
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Divided 1 241.373 267.352 1.10763
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 266.248 23.418
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided 0 7163.55 7759.61 1.08321
273 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 1 241.373 267.352 1.10763
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Subtracted 0 10432.4 11298.4 866
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 1 243.208 266.617 23.409
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Divided 0 12748.1 11770.9 1.08302
274 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Subtracted 11977.8 12842.5 864.7
60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 1 242.744 266.07 23.326
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Divided 0 10432.4 11298.4 1.08301
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 1 241.373 267.352 1.10763
275 40s ribosomal protein s5. [swissprot;acc:p46782] Subtracted 242.473 265.756 23.283
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Divided 241.373 267.352 1.10763
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 10783 11674.1 1.08264
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Subtracted 15977.3 15115.5 861.8
276 60s ribosomal protein l32. [swissprot;acc:p02433] Divided 1 241.13 266.969 1.10716
60s ribosomal protein l9. [swissprot;acc:p32969] 0 10741.6 9922.33 1.08257
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted 1 258.437 235.183 23.254
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 0 12228.2 11367.3 860.9
277 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 18849.7 19704.7 855
40s ribosomal protein s29. [swissprot;acc:p30054] Divided 1 241.849 267.642 1.10665
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 0 11096.8 10251.6 1.08245
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 1 239.277 262.434 23.157
278 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 241.399 267.088 1.10642

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/