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.


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 Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 530 to 579 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
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] 1 225.217 202.459 1.11241
266 transcription factor btf3 homolog 3. [swissprot;acc:q13892] 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 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 0 8054.34 8772.02 1.0891
268 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 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
269 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 1 241.373 267.352 1.10763
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 12463.5 11482.6 1.08542
270 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 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]
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 0 10735.1 9891.37 1.0853
272 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 1 241.373 267.352 1.10763
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 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
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 0 12748.1 11770.9 1.08302
274 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 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 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 10783 11674.1 1.08264
276 60s ribosomal protein l32. [swissprot;acc:p02433] 1 241.13 266.969 1.10716
60s ribosomal protein l9. [swissprot;acc:p32969] 0 10741.6 9922.33 1.08257
277 40s ribosomal protein s29. [swissprot;acc:p30054] 1 241.849 267.642 1.10665
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 0 11096.8 10251.6 1.08245
278 40s ribosomal protein s11. [swissprot;acc:p04643] 1 241.399 267.088 1.10642
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 0 11644 10763.4 1.08181
279 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 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
280 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 0 10620.1 11471.2 1.08014
metastasis-associated protein mta1. [swissprot;acc:q13330] 1 252.512 228.356 1.10578
281 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 0 12522.7 13514.5 1.0792
282 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 1 252.39 228.297 1.10553
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 0 8095.69 8732.68 1.07868
283 60s ribosomal protein l11. [swissprot;acc:p39026] 1 241.828 267.346 1.10552
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 0 11107.1 11959.2 1.07672
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 1 224.657 203.235 1.10541
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 0 14898.9 16041.6 1.0767
285 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 10686 9925.58 1.07661
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 1 224.647 203.242 1.10532
286 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 0 12228.2 11367.3 1.07573
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 1 224.633 203.251 1.1052
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 266.079 1.10517
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 0 17842.7 16590.3 1.07549
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1 240.758 266.078 1.10517
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 0 14930.6 16053 1.07517
289 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 15147.2 14091.9 1.07489
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1 272.781 246.892 1.10486
290 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 0 15147.2 14091.9 1.07489

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/