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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 962 to 1011 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
green
network_comparison
121 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Subtracted Squared 81527.6 56190.6 25337
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided Ranked 269.254 327.655 1.2169
HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Rooted 50.339 62.9975 1.25147
JUNB transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 7488.4 1.3422
PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 199594 130021 1.53509
PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Subtracted Rooted 63.6205 48.8838 14.7367
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked 227.202 192.823 34.379
122 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared 81520.8 56188.5 25332.3
COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked 199.949 234.187 34.238
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Divided Squared 201896 131906 1.53061
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Subtracted Measured 4941.95 7037.11 2095.16
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided 5140.14 6893.53 1.34112
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] Subtracted Rooted 60.9342 75.1387 14.2045
JUND transcription factor jun-d. [swissprot;acc:p17535] Divided 63.636 79.6225 1.25122
KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Ranked 269.248 327.642 1.21688
123 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 24260.3 18172.1 1.33503
CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Subtracted Squared 81478.9 56175.2 25303.7
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Measured 4942.49 7037.32 2094.83
KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided Ranked 269.23 327.601 1.21681
NFYC 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] Subtracted Rooted 46.7419 60.9337 14.1918
PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided Squared 192904 126167 1.52896
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted Ranked 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] Divided Rooted 54.6527 67.9743 1.24375
124 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Subtracted Squared 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] Divided Ranked 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] Subtracted Rooted 46.7419 60.9337 14.1918
PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Divided Squared 192779 126095 1.52884
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted Ranked 285.684 252.234 33.45
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided Rooted 54.6625 67.9477 1.24304
125 AQP5 aquaporin 5. [swissprot;acc:p55064] Subtracted Squared 71388.5 96035.2 24646.7
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided Ranked 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] Divided Squared 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] Subtracted Ranked 285.684 252.234 33.45
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided Rooted 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] Divided Measured 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] Subtracted Ranked 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] Subtracted Measured 450.5 2394.5 1944
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided Ranked 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

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/