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 1075 to 1124 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
269 ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Divided 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
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 0 11644 10763.4 1.08181
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 11107.1 11959.2 852.1
myelin gene expression factor 2. [refseq;acc:nm_016132] 1 235.383 258.476 23.093
279 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Divided 0 10614.2 9812.39 1.08171
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 1 252.644 228.42 1.10605
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Subtracted 0 7621.99 8473.85 851.86
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 1 242.66 265.715 23.055
280 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 0 10620.1 11471.2 1.08014
Subtracted 851.1
metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 1 252.512 228.356 1.10578
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 267.208 244.168 23.04
281 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 22.945
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 241.808 267.335 1.10557
Subtracted 0 11096.8 10251.6 845.2
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Divided 12522.7 13514.5 1.0792

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/