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 Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 377 to 426 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
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 267.352 241.373 25.979
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 198.444 226.582 1.14179
190 fad synthetase. [refseq;acc:nm_025207] Subtracted 267.352 241.373 25.979
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 198.444 226.582 1.14179
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 267.352 241.373 25.979
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 198.444 226.582 1.14179
192 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Subtracted 267.352 241.373 25.979
musashi 2 isoform a. [refseq;acc:nm_138962] Divided 199.458 227.491 1.14055
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 267.352 241.373 25.979
musashi 1. [refseq;acc:nm_002442] Divided 199.458 227.491 1.14055
194 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted 267.352 241.373 25.979
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 199.458 227.491 1.14055
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 267.352 241.373 25.979
huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 200.417 227.971 1.13748
196 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 231.407 263.215 1.13745
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Subtracted 246.892 272.781 25.889
197 60s ribosomal protein l32. [swissprot;acc:p02433] 266.969 241.13 25.839
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Divided 231.407 263.215 1.13745
198 40s ribosomal protein s29. [swissprot;acc:p30054] Subtracted 267.642 241.849 25.793
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 231.394 263.191 1.13741
199 40s ribosomal protein s11. [swissprot;acc:p04643] Subtracted 267.088 241.399 25.689
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 276.059 242.735 1.13729
200 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted 267.335 241.808 25.527
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 276.018 242.718 1.1372
201 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted 267.346 241.828 25.518
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 211.382 240.133 1.13601
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 266.079 240.758 25.321
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 228.784 201.478 1.13553
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 266.078 240.758 25.32
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 228.752 201.515 1.13516
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 243.588 268.632 25.044
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 228.752 201.515 1.13516
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 243.592 268.635 25.043
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 200.968 228.1 1.13501
206 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 266.414 241.411 25.003
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided 201.006 228.085 1.13472
207 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 212.363 237.312 24.949
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 252.234 285.684 1.13261
208 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 265.717 240.782 24.935
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 252.234 285.684 1.13261
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 265.717 240.782 24.935
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 252.234 285.684 1.13261
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617]
rna-binding protein. [refseq;acc:nm_019027] Subtracted 212.41 237.302 24.892
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 252.234 285.684 1.13261
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 212.41 237.302 24.892
213 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 186.95 210.693 1.127

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/