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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 982 to 1031 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
123 PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared Divided 192904 126167 1.52896
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked Subtracted 227.032 193.056 33.976
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted Divided 54.6527 67.9743 1.24375
124 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared Subtracted 71389.9 96037.6 24647.7
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured 4944.3 7038.04 2093.74
HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Ranked Divided 208.52 171.595 1.21519
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 18168.9 1.33501
NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Rooted Subtracted 46.7419 60.9337 14.1918
PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Divided 192779 126095 1.52884
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked Subtracted 285.684 252.234 33.45
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted Divided 54.6625 67.9477 1.24304
125 AQP5 aquaporin 5. [swissprot;acc:p55064] Squared Subtracted 71388.5 96035.2 24646.7
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Ranked Divided 208.588 171.778 1.21429
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 18168.9 1.33501
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted 12471.7 14561.7 2090
RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared Divided 189976 124480 1.52616
SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Ranked Subtracted 285.684 252.234 33.45
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Divided 54.8203 67.934 1.23921
SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Subtracted 35.6294 49.8119 14.1825
126 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared 71387.4 96033.4 24646
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured Divided 24250 18164.9 1.33499
FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked Subtracted 285.684 252.234 33.45
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 14.1587
HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided 60.9342 75.1387 1.23311
PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 189976 124480 1.52616
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Measured Subtracted 450.5 2394.5 1944
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked Divided 94 114 1.21277
127 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 88432.6 58423.3 1.51365
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked 94 114 1.21277
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Subtracted 285.684 252.234 33.45
DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 13.58
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided 60.9353 75.094 1.23236
JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 7523.39 1.33436
MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared Subtracted 71386.9 96032.5 24645.6
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Measured 450.5 2394.5 1944
128 no value pnas-18. [sptrembl;acc:q9bzu3] Squared Divided 87787.3 58155.8 1.50952
AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Subtracted 71346.6 95965.1 24618.5
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured Divided 4355.61 5810.82 1.3341
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked Subtracted 285.684 252.234 33.45
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided 94 114 1.21277
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 1.23069
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured Subtracted 11004.2 12944.2 1940
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 67.9743 13.3216
129 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 252.234 33.45
LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured Divided 4358.13 5811.49 1.33348
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 66.7323 1.23044
PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 178263 118639 1.50257
PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured Subtracted 15274.9 13346.9 1928
SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared 71062.4 95488.9 24426.5
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 67.9477 13.2852

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/