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 4741 to 4790 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
593 HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured Divided 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
HTATSF1 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Ranked Subtracted 217.67 230.596 12.926
NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured 6770.78 7517.97 747.19
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] Divided 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
CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Squared Subtracted 30999.6 35666.3 4666.7
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Ranked 207.26 194.346 12.914
KPNA1 importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared Divided 23517.1 27867.3 1.18498
LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Rooted Subtracted 54.4927 49.6125 4.8802
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Measured 6089.21 6835.34 746.13
595 no value histone h2b. [refseq;acc:nm_175055] Divided 3946.32 4475.47 1.13409
ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Ranked Subtracted 207.26 194.346 12.914
FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Rooted Divided 51.2427 55.468 1.08246
FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Subtracted 54.4927 49.6125 4.8802
PGLS 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Squared 29345.7 34004.2 4658.5
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Divided 34129.7 40434.8 1.18474
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Measured Subtracted 6088.77 6834.87 746.1
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Ranked Divided 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
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked Subtracted 207.26 194.346 12.914
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Squared 31583.4 36221.8 4638.4
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted 54.4927 49.6125 4.8802
PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Measured 4533.74 5279.4 745.66
PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Squared Divided 34129.6 40434.5 1.18473
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Ranked 212.253 199.908 1.06175
597 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured Subtracted 4533.74 5279.4 745.66
histone h2b.d (h2b/d). [swissprot;acc:q99877] Divided 3946.32 4475.47 1.13409
GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Rooted 60.0587 65.0057 1.08237
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Ranked Subtracted 207.26 194.346 12.914
LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted 54.4927 49.6125 4.8802
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Squared Divided 34129.4 40434.2 1.18473
VAV2 vav-2 protein. [swissprot;acc:p52735] Ranked 212.526 200.212 1.0615
VCL vinculin (metavinculin). [swissprot;acc:p18206] Squared Subtracted 27463 32090.3 4627.3
598 no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured 4533.74 5279.4 745.66
AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Ranked Divided 248.463 234.095 1.06138
GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Subtracted 207.261 194.347 12.914
HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Measured Divided 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
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared Subtracted 14728.8 19330.8 4602
PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 34129.6 40434.5 1.18473
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted Subtracted 54.4927 49.6125 4.8802
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 Divided 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
CRKL crk-like protein. [swissprot;acc:p46109] Ranked Subtracted 207.26 194.346 12.914
ESRRB steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Rooted 82.3879 87.2663 4.8784
G6PD glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Squared 28767.1 33317.5 4550.4
HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Measured Divided 3946.32 4475.47 1.13409

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/