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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 980 to 1029 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Value Type
red
network_comparison
green
123 KCND1 Divided potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked 269.23 1.21681 327.601
NFYC Subtracted nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Rooted 46.7419 14.1918 60.9337
PPP1R2 Divided protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 192904 1.52896 126167
SNRPD1 Subtracted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked 227.032 33.976 193.056
TIA1 Divided nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 1.24375 67.9743
124 AQP4 Subtracted aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared 71389.9 24647.7 96037.6
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured 4944.3 2093.74 7038.04
HMG20B Divided 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 208.52 1.21519 171.595
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 1.33501 18168.9
NFYA Subtracted 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 46.7419 14.1918 60.9337
PPP1R2P9 Divided type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared 192779 1.52884 126095
PSEN2 Subtracted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked 285.684 33.45 252.234
TIAL1 Divided nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 1.24304 67.9477
125 AQP5 Subtracted aquaporin 5. [swissprot;acc:p55064] Squared 71388.5 24646.7 96035.2
HMG20A Divided high-mobility group 20a. [refseq;acc:nm_018200] Ranked 208.588 1.21429 171.778
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 1.33501 18168.9
NFU1 Subtracted hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 12471.7 2090 14561.7
RRS1 Divided ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 189976 1.52616 124480
SKP1A Subtracted 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 285.684 33.45 252.234
SNRPD1 Divided small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted 54.8203 1.23921 67.934
SON Subtracted 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] 35.6294 14.1825 49.8119
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 24646 96033.4
ATG4B Divided cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured 24250 1.33499 18164.9
FBXW7 Subtracted 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 285.684 33.45 252.234
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 14.1587 75.094
HMG20B Divided 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] 60.9342 1.23311 75.1387
PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 189976 1.52616 124480
RINT1 Subtracted rad50-interacting protein 1. [refseq;acc:nm_021930] Measured 450.5 1944 2394.5
STAMBPL1 Divided associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked 94 1.21277 114
127 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 88432.6 1.51365 58423.3
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked 94 1.21277 114
CUL2 Subtracted cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 33.45 252.234
DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 13.58 166.771
HMG20A Divided high-mobility group 20a. [refseq;acc:nm_018200] 60.9353 1.23236 75.094
JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 1.33436 7523.39
MIP Subtracted lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared 71386.9 24645.6 96032.5
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Measured 450.5 1944 2394.5
128 no value Divided pnas-18. [sptrembl;acc:q9bzu3] Squared 87787.3 1.50952 58155.8
AQP1 Subtracted aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 71346.6 24618.5 95965.1
LUC7L2 Divided luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 4355.61 1.3341 5810.82
PSEN1 Subtracted presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 33.45 252.234
STAMBP Divided associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 94 1.21277 114
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 1.23069 39.0445
TCP1 Subtracted t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured 11004.2 1940 12944.2
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 13.3216 67.9743
129 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 33.45 252.234
LUC7L Divided luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 4358.13 1.33348 5811.49
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 1.23044 66.7323
PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 178263 1.50257 118639
PPP1R13B Subtracted protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured 15274.9 1928 13346.9

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/