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 Gene Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
green
red
network_comparison
263 Squared adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 20236.2 26157.6 1.29261
Rooted paxillin. [swissprot;acc:p49023] 66.7002 59.4073 1.12276
264 Measured cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4094.57 4987.58 1.2181
Ranked mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 196.978 219.421 1.11394
Squared adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 20236.2 26157.6 1.29261
Rooted wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 74.1438 66.1122 1.12148
265 Measured wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 20369.9 24806.9 1.21782
Ranked splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 202.459 225.217 1.11241
Squared leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 20236.2 26157.6 1.29261
Rooted u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 62.8281 56.031 1.12131
266 Measured cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 20369.9 24806.9 1.21782
Ranked transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 267.88 241.07 1.11121
Squared fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 20236.2 26157.6 1.29261
Rooted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 74.1074 66.1064 1.12103
267 Measured ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 11523 14021.4 1.21682
Ranked density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 267.88 241.07 1.11121
Squared leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 20236.2 26157.6 1.29261
Rooted tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 74.1073 66.1064 1.12103
268 Measured cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 20127.8 24473.9 1.21593
Ranked eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 244.167 271.016 1.10996
Squared laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 20236.2 26157.6 1.29261
Rooted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 74.1074 66.1064 1.12103
269 Measured u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 5575.52 4590.18 1.21466
Ranked cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 267.352 241.373 1.10763
Squared thymic stromal co-transporter. [refseq;acc:nm_033051] 20236.2 26157.6 1.29261
Rooted tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 74.1074 66.1064 1.12103
270 Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 19479.8 23640.2 1.21358
Ranked fad synthetase. [refseq;acc:nm_025207] 267.352 241.373 1.10763
Squared transcription factor iib. [refseq;acc:nm_013242] 50300.6 64739.9 1.28706
Rooted crk-like protein. [swissprot;acc:p46109] 74.1074 66.1064 1.12103
271 Measured chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 3093.78 2554.89 1.21092
Ranked bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 267.352 241.373 1.10763
Squared splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] 50300.6 64739.9 1.28706
Rooted proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 74.1073 66.1064 1.12103
272 Measured histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 4669.27 3858.52 1.21012
Ranked ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 267.352 241.373 1.10763
Squared adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 46971.1 36563.7 1.28464
Rooted proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 74.1074 66.1064 1.12103
273 Measured eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3870.8 3199.4 1.20985
Ranked bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 267.352 241.373 1.10763
Squared filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 20665.7 16120.1 1.28198
Rooted proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 74.1074 66.1064 1.12103
274 Measured chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 2579.49 3119.98 1.20953
Ranked nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 267.352 241.373 1.10763
Squared rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 20665.7 16120.1 1.28198
Rooted 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] 74.1068 66.1063 1.12102
275 Measured regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 2579.49 3119.98 1.20953
Ranked cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 267.352 241.373 1.10763
Squared protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 20665.7 16120.1 1.28198
Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 74.0977 66.1048 1.12091

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/