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 Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 518 to 567 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
259 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 204.37 227.999 1.11562
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 219.421 1.11394
surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 265.696 242.14 23.556
261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Divided 196.978 219.421 1.11394
zinc finger protein 291. [swissprot;acc:q9by12] Subtracted 265.696 242.14 23.556
262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided 196.978 219.421 1.11394
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted 265.696 242.14 23.556
263 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided 196.978 219.421 1.11394
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Subtracted 265.696 242.14 23.556
264 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 266.796 243.24
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided 196.978 219.421 1.11394
265 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 263.798 240.243 23.555
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided 202.459 225.217 1.11241
266 ribosomal protein l10-like protein. [refseq;acc:nm_080746] Subtracted 266.662 243.12 23.542
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 267.88 241.07 1.11121
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 266.661 243.12 23.541
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Divided 267.88 241.07 1.11121
268 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 244.167 271.016 1.10996
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 265.136 241.625 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 267.352 241.373 1.10763
270 40s ribosomal protein s3. [swissprot;acc:p23396] Subtracted 265.119 241.612 23.507
fad synthetase. [refseq;acc:nm_025207] Divided 267.352 241.373 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]
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 266.559 243.072 23.487
272 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Divided 267.352 241.373 1.10763
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 266.248 242.83 23.418
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] Divided 267.352 241.373 1.10763
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Subtracted 266.617 243.208 23.409
274 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 266.07 242.744 23.326
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Divided 267.352 241.373 1.10763
275 40s ribosomal protein s5. [swissprot;acc:p46782] Subtracted 265.756 242.473 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 267.352 241.373 1.10763
276 60s ribosomal protein l32. [swissprot;acc:p02433] 266.969 241.13 1.10716
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted 235.183 258.437 23.254
277 40s ribosomal protein s29. [swissprot;acc:p30054] Divided 267.642 241.849 1.10665
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 262.434 239.277 23.157
278 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 267.088 241.399 1.10642
myelin gene expression factor 2. [refseq;acc:nm_016132] Subtracted 258.476 235.383 23.093
279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 228.42 252.644 1.10605
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Subtracted 265.715 242.66 23.055
280 metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 228.356 252.512 1.10578
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 244.168 267.208 23.04
281 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 265.104 242.159 22.945
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 267.335 241.808 1.10557
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] 228.297 252.39 1.10553
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Subtracted 265.104 242.159 22.945
283 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 265.255 242.37 22.885
60s ribosomal protein l11. [swissprot;acc:p39026] Divided 267.346 241.828 1.10552
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 203.235 224.657 1.10541

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/