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 Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1108 to 1157 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
Value Type
description
red
network_comparison
green
139 Divided ZC3H14 Rooted nuclear protein ukp68. [refseq;acc:nm_024824] 54.9787 1.20486 66.2416
Subtracted CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 49.3267 13.09 62.4167
CDC2 Measured cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 12780.7 1904.3 10876.4
CHRAC1 Ranked chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 287.41 30.575 256.835
STAM Squared signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] 86861.5 21491.8 65369.7
140 Divided CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 81527.6 1.45091 56190.6
FLNB Rooted 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] 55.6161 1.19989 66.7332
KCNIP2 Measured kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 2760.28 1.31425 2100.27
RRAGA Ranked ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 59 1.20408 49
Subtracted HLX Measured homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 1899 698.5
NCBP2 Ranked 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 228.306 30.295 198.011
PRKCH Squared protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] 86609.4 21374.9 65234.5
UNC84A Rooted sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 39.9725 13.0248 52.9973
141 Divided CCNB1 Squared g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 81520.8 1.45084 56188.5
REV1 Rooted rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 55.6161 1.19989 66.7332
RRAGC Ranked ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 59 1.20408 49
SNRPD2 Measured small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 4405.4 1.3125 5782.08
Subtracted COMP Ranked cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 29.247 269.238
HBS1L Measured hbs1-like. [refseq;acc:nm_006620] 2597.5 1899 698.5
PRKCE Squared protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] 86600.9 21371 65229.9
STAMBPL1 Rooted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 105.205 12.9635 92.2415
142 Divided CDC2 Squared cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 81478.9 1.45044 56175.2
PITRM1 Measured metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 1.30832 7090.37
PRMT1 Rooted protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 55.6161 1.19989 66.7332
RRAGB Ranked ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 59 1.20408 49
Subtracted CHMP2A Rooted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 105.205 12.9635 92.2415
JUND Measured transcription factor jun-d. [swissprot;acc:p17535] 5638.2 1885.19 7523.39
PPIB Squared peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 86600.9 21371 65229.9
THBS3 Ranked thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 29.244 269.234
143 Divided ALG1 Measured beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 9275.1 1.30826 7089.65
ANLN Ranked anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 59 1.20408 49
PPP1R13B Squared protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 124319 1.43145 86848.2
PRMT8 Rooted protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 55.6161 1.19989 66.7332
Subtracted CSTF2 Measured cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 15427.2 1854.4 13572.8
OGT Squared udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] 86600.9 21371 65229.9
SF4 Ranked splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 28.751 211.382
STAMBP Rooted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 105.205 12.9635 92.2415
144 Divided KCNIP1 Ranked kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 265.686 1.20312 319.651
SNRP70 Rooted u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 55.6161 1.19989 66.7332
TP53BP2 Squared tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 123324 1.42938 86277.9
UNC84A Measured sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 3349.9 1.30231 4362.61
Subtracted COX4I1 Squared cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 86600.9 21371 65229.9
CSRP1 Ranked cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 28.565 267.915
TIA1 Measured nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 4133.47 1811.85 5945.32
VPS24 Rooted neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 105.205 12.9635 92.2415
145 Divided no value Measured ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 16771.5 1.30122 12889.1
Squared nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 310840 1.42515 442993
Rooted filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 55.6161 1.19989 66.7332
KCNIP4 Ranked potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 265.639 1.20293 319.546
Subtracted CHMP4A Rooted protein hspc134 (protein cda04). [swissprot;acc:q9by43] 105.205 12.9635 92.2415

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/