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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2364 to 2413 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
591 Rooted leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 108.659 100.356 1.08274
592 Measured histone h2b.c (h2b/c). [swissprot;acc:q99880] 3946.32 4475.47 1.13409
Ranked protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 91.63 97.4011 1.06298
Squared voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] 23526.4 27879.3 1.18502
Rooted ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 108.659 100.356 1.08274
593 Measured histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 3946.32 4475.47 1.13409
Ranked tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
Squared aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 23526.4 27879.3 1.18502
Rooted transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 108.653 100.352 1.08272
594 Measured histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 3946.32 4475.47 1.13409
Ranked pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
Squared importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 23517.1 27867.3 1.18498
Rooted transforming protein n-ras. [swissprot;acc:p01111] 108.65 100.35 1.08271
595 Measured histone h2b. [refseq;acc:nm_175055] 3946.32 4475.47 1.13409
Ranked vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 1.0618
Squared 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 34129.7 40434.8 1.18474
Rooted fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 51.2427 55.468 1.08246
596 Measured histone h2b.s (h2b/s). [swissprot;acc:p57053] 3946.32 4475.47 1.13409
Ranked vav-3 protein. [swissprot;acc:q9ukw4] 212.253 199.908 1.06175
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

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/