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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2362 to 2411 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
591 HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Measured 6740.5 7644.76 1.13415
RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Ranked 216.72 230.439 1.0633
SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted 108.659 100.356 1.08274
592 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]
HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Measured 3946.32 4475.47 1.13409
KCNAB2 voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Squared 23526.4 27879.3 1.18502
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Ranked 91.63 97.4011 1.06298
593 AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Squared 23526.4 27879.3 1.18502
DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Ranked 232.118 218.406 1.06278
HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured 3946.32 4475.47 1.13409
HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted 108.653 100.352 1.08272
594 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Measured 3946.32 4475.47 1.13409
transforming protein n-ras. [swissprot;acc:p01111] Rooted 108.65 100.35 1.08271
CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Ranked 223.282 210.136 1.06256
KPNA1 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared 23517.1 27867.3 1.18498
595 no value histone h2b. [refseq;acc:nm_175055] Measured 3946.32 4475.47 1.13409
FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Rooted 51.2427 55.468 1.08246
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 34129.7 40434.8 1.18474
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Ranked 212.2 199.849 1.0618
596 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Rooted 60.0587 65.0057 1.08237
histone h2b.s (h2b/s). [swissprot;acc:p57053] Measured 3946.32 4475.47 1.13409
PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Squared 34129.6 40434.5 1.18473
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Ranked 212.253 199.908 1.06175
597 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] Measured 3946.32 4475.47 1.13409
GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Rooted 60.0587 65.0057 1.08237
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Squared 34129.4 40434.2 1.18473
VAV2 vav-2 protein. [swissprot;acc:p52735] Ranked 212.526 200.212 1.0615
598 AKT1 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
HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Measured 3946.32 4475.47 1.13409
MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Rooted 61.2527 66.2644 1.08182
PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Squared 34129.6 40434.5 1.18473
599 AKT3 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] Ranked 248.463 234.095 1.06138
CPSF4 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] Rooted 138.375 127.926 1.08168
HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Measured 3946.32 4475.47 1.13409
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Squared 34129.6 40434.5 1.18473
600 no value histone h2b.e (h2b/e). [swissprot;acc:q99879] Measured 3946.32 4475.47 1.13409
AKT2 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] Ranked 248.463 234.095 1.06138
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Rooted 138.375 127.926 1.08168
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Squared 34129.6 40434.5 1.18473
601 PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
SYMPK symplekin. [swissprot;acc:q92797] Measured 15213.4 13418.1 1.1338
VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Ranked 206.274 218.792 1.06069
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Rooted 138.032 127.651 1.08132
602 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Measured 4864.66 5514.87 1.13366
CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 127.651 1.08132
MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Ranked 206.274 218.792 1.06069
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Squared 19129.8 22652.9 1.18417
603 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Measured 4864.66 5514.87 1.13366
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Squared 34071.5 40336.5 1.18388
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Rooted 60.0742 64.9418 1.08103

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/