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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2375 to 2424 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
594 CDC40 Ranked pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
KPNA1 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
595 no value Measured histone h2b. [refseq;acc:nm_175055] 3946.32 4475.47 1.13409
FBL Rooted fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 51.2427 55.468 1.08246
PRKAA2 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
VAV1 Ranked vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 1.0618
596 no value Measured histone h2b.s (h2b/s). [swissprot;acc:p57053] 3946.32 4475.47 1.13409
Rooted cbf1 interacting corepressor. [refseq;acc:nm_004882] 60.0587 65.0057 1.08237
PRKAG1 Squared 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 34129.6 40434.5 1.18473
VAV3 Ranked vav-3 protein. [swissprot;acc:q9ukw4] 212.253 199.908 1.06175
597 no value Measured histone h2b.d (h2b/d). [swissprot;acc:q99877] 3946.32 4475.47 1.13409
GPATCH1 Rooted evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] 60.0587 65.0057 1.08237
PRKAA1 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
VAV2 Ranked vav-2 protein. [swissprot;acc:p52735] 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 Measured histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 3946.32 4475.47 1.13409
MARS Rooted methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 61.2527 66.2644 1.08182
PRKAB2 Squared 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 34129.6 40434.5 1.18473
599 AKT3 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
CPSF4 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
HIST1H2BA Measured testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 3946.32 4475.47 1.13409
PRKAG3 Squared 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 34129.6 40434.5 1.18473
600 no value Measured histone h2b.e (h2b/e). [swissprot;acc:q99879] 3946.32 4475.47 1.13409
AKT2 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
KIAA1012 Rooted trs85 homolog. [swissprot;acc:q9y2l5] 138.375 127.926 1.08168
PRKAB1 Squared 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 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 Measured symplekin. [swissprot;acc:q92797] 15213.4 13418.1 1.1338
VPS39 Ranked vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] 206.274 218.792 1.06069
WDR33 Rooted wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 138.032 127.651 1.08132
602 ATXN2L Measured ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 4864.66 5514.87 1.13366
CPSF1 Rooted cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 138.032 127.651 1.08132
MAP4 Ranked microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] 206.274 218.792 1.06069
TXNL4A 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
603 no value Measured ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 4864.66 5514.87 1.13366
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
LEF1 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
604 no value Squared alpha-nac protein. [sptrembl;acc:q9h009] 34069.4 40333 1.18385
RPL15 Ranked 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602
SLU7 Rooted step ii splicing factor slu7. [refseq;acc:nm_006425] 60.0742 64.9418 1.08103
VCL Measured vinculin (metavinculin). [swissprot;acc:p18206] 5958.23 6743.37 1.13177
605 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 6143.52 6950.75 1.1314
DIRAS1 Squared small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] 34068.1 40330.8 1.18383
HIST1H2BL Ranked histone h2b.c (h2b/c). [swissprot;acc:q99880] 247.47 233.441 1.0601
ZNF547 Rooted sedlin. [swissprot;acc:o14582] 116.061 125.434 1.08076
606 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
ATP2C1 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
DIRAS2 Squared di-ras2. [refseq;acc:nm_017594] 34068 40330.7 1.18383
HIST2H2BA Ranked histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 247.47 233.441 1.0601

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/