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 Network Comparison Type Value Type Interaction Map red network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 375 to 424 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
188 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted 227.357 26.793 254.15
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 226.582 1.14179 198.444
189 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Subtracted 241.373 25.979 267.352
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 1.14179 198.444
190 fad synthetase. [refseq;acc:nm_025207] Subtracted 241.373 25.979 267.352
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 226.582 1.14179 198.444
191 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] Subtracted 241.373 25.979 267.352
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 226.582 1.14179 198.444
192 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Subtracted 241.373 25.979 267.352
musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 1.14055 199.458
193 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] Subtracted 241.373 25.979 267.352
musashi 1. [refseq;acc:nm_002442] Divided 227.491 1.14055 199.458
194 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted 241.373 25.979 267.352
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 227.491 1.14055 199.458
195 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Subtracted 241.373 25.979 267.352
huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 227.971 1.13748 200.417
196 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 1.13745 231.407
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Subtracted 272.781 25.889 246.892
197 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 25.839 266.969
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Divided 263.215 1.13745 231.407
198 40s ribosomal protein s29. [swissprot;acc:p30054] Subtracted 241.849 25.793 267.642
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 263.191 1.13741 231.394
199 40s ribosomal protein s11. [swissprot;acc:p04643] Subtracted 241.399 25.689 267.088
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 242.735 1.13729 276.059
200 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted 241.808 25.527 267.335
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 242.718 1.1372 276.018
201 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted 241.828 25.518 267.346
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 1.13601 211.382
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 240.758 25.321 266.079
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 1.13553 228.784
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 240.758 25.32 266.078
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 201.515 1.13516 228.752
204 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 268.632 25.044 243.588
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 201.515 1.13516 228.752
205 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Subtracted 268.635 25.043 243.592
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 228.1 1.13501 200.968
206 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 241.411 25.003 266.414
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided 228.085 1.13472 201.006
207 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 237.312 24.949 212.363
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 285.684 1.13261 252.234
208 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 240.782 24.935 265.717
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Divided 285.684 1.13261 252.234
209 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted 240.782 24.935 265.717
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Divided 285.684 1.13261 252.234
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617]
rna-binding protein. [refseq;acc:nm_019027] Subtracted 237.302 24.892 212.41
211 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided 285.684 1.13261 252.234
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 237.302 24.892 212.41

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/