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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 375 to 424 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
188 GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted 227.357 254.15 26.793
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 226.582 198.444 1.14179
189 PCYT1A 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 241.373 267.352 25.979
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 198.444 1.14179
190 FLAD1 fad synthetase. [refseq;acc:nm_025207] Subtracted 241.373 267.352 25.979
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 226.582 198.444 1.14179
191 no value 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 241.373 267.352 25.979
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 226.582 198.444 1.14179
192 LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Subtracted 241.373 267.352 25.979
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 199.458 1.14055
193 MSI1 musashi 1. [refseq;acc:nm_002442]
PAPSS1 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 241.373 267.352 25.979
194 POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Divided 227.491 199.458 1.14055
195 PCYT1B 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 241.373 267.352 25.979
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 227.971 200.417 1.13748
196 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Subtracted 272.781 246.892 25.889
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 263.215 231.407 1.13745
197 FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]
SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Subtracted 241.13 266.969 25.839
198 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 25.793
FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 263.191 231.394 1.13741
199 EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 242.735 276.059 1.13729
RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Subtracted 241.399 267.088 25.689
200 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 25.527
EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 242.718 276.018 1.1372
201 RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted 241.828 267.346 25.518
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 211.382 1.13601
202 RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 240.758 266.079 25.321
TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 228.784 1.13553
203 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 240.758 266.078 25.32
TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 201.515 228.752 1.13516
204 CAPN2 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 268.632 243.588 25.044
TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 201.515 228.752 1.13516
205 CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Subtracted 268.635 243.592 25.043
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 228.1 200.968 1.13501
206 LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 201.006 1.13472
RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 241.411 266.414 25.003
207 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 24.949
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 285.684 252.234 1.13261
208 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 240.782 265.717 24.935
SKP1A 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 285.684 252.234 1.13261
209 BCCIP 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 240.782 265.717 24.935
FBXW7 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 285.684 252.234 1.13261
210 no value rna-binding protein. [refseq;acc:nm_019027] Subtracted 237.302 212.41 24.892
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Divided 285.684 252.234 1.13261
211 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 237.302 212.41 24.892
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided 285.684 252.234 1.13261
212 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 237.302 212.41 24.892

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
- Hugo is the HGNC identifier if it exists
- 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/