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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Value Type Interaction Map Gene green Rank Filtered description Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 1130 to 1179 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
green
Rank
description
network_comparison
red
204.964 967 protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 1.03426 211.987
968 numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
969 tbc1 domain family member 5. [swissprot;acc:q92609]
970 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972 numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975 protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
205.083 941 swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 1.03586 212.437
944 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
205.085 945 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 212.44
205.087 943 sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 212.442
205.088 940 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]
942 grancalcin. [swissprot;acc:p28676]
205.168 2638 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] 1.00125 204.911
205.191 947 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 1.03567 212.51
205.286 435 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 1.07909 221.522
436 paxillin. [swissprot;acc:p49023]
2459 phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 1.00309 204.653
205.292 918 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 1.03731 212.952
205.326 2454 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 1.00314 204.683
2455 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]
2456 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]
2458 solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183]
205.329 1402 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] 1.0212 209.682
205.332 2453 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 1.00315 204.688
205.333 2451 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]
2452 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
205.371 2449 phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] 1.00319 204.717
205.376 2287 phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] 1.00535 206.475
205.38 2296 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] 1.00521 206.451
205.466 953 polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] 1.03512 198.494
205.556 172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 1.17685 174.667
205.747 2094 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 1.00765 207.321
205.9 421 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 1.08403 223.202
205.923 2063 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] 1.00833 207.638
205.939 2064 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 207.655
205.948 2054 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 1.00834 207.665
205.95 2052 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 207.667
206.078 648 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 1.05895 218.227
206.195 691 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 1.05532 217.602
692 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
206.305 2133 orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] 1.00696 207.74
206.308 2135 nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] 207.743
206.339 1096 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 1.02911 212.345
206.343 2141 orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] 1.00689 207.765
206.41 2003 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 1.00923 208.315
206.51 2547 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 1.00186 206.894
206.516 2548 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 1.00185 206.899

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/