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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4391 to 4440 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
596 Squared 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 34129.6 40434.5 1.18473
Rooted cbf1 interacting corepressor. [refseq;acc:nm_004882] 60.0587 65.0057 1.08237
597 Measured histone h2b.d (h2b/d). [swissprot;acc:q99877] 3946.32 4475.47 1.13409
Ranked vav-2 protein. [swissprot;acc:p52735] 212.526 200.212 1.0615
Squared 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 34129.4 40434.2 1.18473
Rooted evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 60.0587 65.0057 1.08237
598 Measured histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 3946.32 4475.47 1.13409
Ranked rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 1.06138
Squared 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 34129.6 40434.5 1.18473
Rooted methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 61.2527 66.2644 1.08182
599 Measured testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 3946.32 4475.47 1.13409
Ranked rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] 248.463 234.095 1.06138
Squared 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 34129.6 40434.5 1.18473
Rooted cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 138.375 127.926 1.08168
600 Measured histone h2b.e (h2b/e). [swissprot;acc:q99879] 3946.32 4475.47 1.13409
Ranked rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] 248.463 234.095 1.06138
Squared 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 34129.6 40434.5 1.18473
Rooted trs85 homolog. [swissprot;acc:q9y2l5] 138.375 127.926 1.08168
601 Measured symplekin. [swissprot;acc:q92797] 15213.4 13418.1 1.1338
Ranked vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] 206.274 218.792 1.06069
Squared 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 34129.6 40434.5 1.18473
Rooted wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 138.032 127.651 1.08132
602 Measured ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 4864.66 5514.87 1.13366
Ranked microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] 206.274 218.792 1.06069
Squared spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 19129.8 22652.9 1.18417
Rooted cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 138.032 127.651 1.08132
603 Measured ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 4864.66 5514.87 1.13366
Ranked lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 225.829 212.945 1.0605
Squared nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 34071.5 40336.5 1.18388
Rooted u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 60.0742 64.9418 1.08103
604 Measured vinculin (metavinculin). [swissprot;acc:p18206] 5958.23 6743.37 1.13177
Ranked 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602
Squared alpha-nac protein. [sptrembl;acc:q9h009] 34069.4 40333 1.18385
Rooted step ii splicing factor slu7. [refseq;acc:nm_006425] 60.0742 64.9418 1.08103
605 Measured probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 6143.52 6950.75 1.1314
Ranked histone h2b.c (h2b/c). [swissprot;acc:q99880] 247.47 233.441 1.0601
Squared small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 34068.1 40330.8 1.18383
Rooted sedlin. [swissprot;acc:o14582] 116.061 125.434 1.08076
606 Measured calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 6148.94 6955.76 1.13121
Ranked histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 247.47 233.441 1.0601
Squared di-ras2. [refseq;acc:nm_017594] 34068 40330.7 1.18383
Rooted synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 116.061 125.434 1.08076
607 Measured likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 14976.4 13246.6 1.13058
Ranked histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 247.47 233.441 1.0601
Squared cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 26583.8 31468.6 1.18375
Rooted bet3 homolog. [swissprot;acc:o43617] 116.061 125.434 1.08076
608 Measured nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 4510.61 5098.74 1.13039
Ranked histone h2b. [refseq;acc:nm_175055] 247.47 233.441 1.0601
Squared nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 24560.6 29071.1 1.18365
Rooted splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 59.6517 64.4642 1.08068

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/