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 [...,...].
green network_comparison Filtered Value Type description Network Comparison Type Interaction Map Rank red Gene
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
green  : 0
network_comparison  : 0
Filtered  : 1
Value Type  : Measured
Network Comparison Type  : Subtracted
red  : 0
description
Interaction Map
Rank
transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444] High confidence 2792
transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3] 2790
transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3] 2778
transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [swissprot;acc:q9uh92] 3091
transcription initiation factor iia alpha and beta chains (tfiia p35 and p19 subunits) (tfiia-42) (tfiial). [swissprot;acc:p52655] 2848
transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657] 2946
transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [swissprot;acc:p29083] 2894
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 3178
transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] 2941
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 2999
transcription initiation factor tfiid 30 kda subunit (tafii-30) (tafii30). [swissprot;acc:q12962] 2839
transcription termination factor, rna polymerase ii; lodestar protein. [refseq;acc:nm_003594] 3043
transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [refseq;acc:nm_057175] 2854
transcriptional repressor nac1. [refseq;acc:nm_052876] 2872
transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [swissprot;acc:q12986] 3169
transforming growth factor beta 1 precursor (tgf-beta 1). [swissprot;acc:p01137] 3105
transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [swissprot;acc:p08112] 3155
transforming growth factor beta 3 precursor (tgf-beta 3). [swissprot;acc:p10600] 3035
transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45] 3174
transmembrane protein 4. [refseq;acc:nm_014255] 2923
transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766] 3041
Low confidence 5043
trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494] High confidence 3159
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] 2945
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 2931
tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] 2833
tu12b1-ty protein. [refseq;acc:nm_016575] 3074
tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [swissprot;acc:p05214] 3175
tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922] 3141
Low confidence 5052
tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347] High confidence 2817
tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] 2858
ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995] 3192
ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974] 3075
ubiquitin protein ligase. [refseq;acc:nm_130466] 2902
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 2828
ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] 3094
ubiquitin-like protein nedd8. [swissprot;acc:q15843] 3001
udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] 2810
udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224] 2835
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 3085
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 2819
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 3086
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 2793
udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [swissprot;acc:q9by64] 2979
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 2889
udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662] 2818
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 3030
uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533] 2772
uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132] 3010

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/