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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Network Comparison Type Value Type Gene green description Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 1530 to 1579 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
green
description
Rank
network_comparison
red
212.567 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 1730 1.01303 215.336
212.572 s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 2555 1.00179 212.953
212.575 mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 1299 1.0238 217.635
212.576 mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 1300 1.02379 217.634
212.584 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 1302 1.02371 217.624
212.596 itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] 1635 1.01494 215.772
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 1634
212.618 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] 938 1.03588 220.246
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] 937
212.656 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 1126 1.02742 218.487
212.672 cellular modulator of immune recognition. [refseq;acc:nm_145021] 1179 1.02593 218.186
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 1178
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 1181
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] 1177
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] 1176
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 1175
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] 1180
212.675 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 1132 1.02731 218.484
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 1140
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 1139
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 1141
sec13-related protein. [swissprot;acc:p55735] 1133
secretory pathway component sec31b-1. [refseq;acc:nm_015490] 1143
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 1135
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] 1142
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] 1138
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] 1145 1.0273 218.481
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] 1137 1.02731 218.484
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] 1131
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] 1134
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] 1144
yeast sec31p homolog. [refseq;acc:nm_014933] 1136
212.676 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 1120 1.02752 218.528
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] 1146 1.0273 218.483
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] 1121 1.02752 218.529
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 1119 218.528
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] 1122 1.02751 218.527
212.806 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 866 1.03994 221.306
212.875 step ii splicing factor slu7. [refseq;acc:nm_006425] 752 1.04974 223.463
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 751
212.888 succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] 1207 1.02525 207.644
212.891 integral membrane protein cii-3b. [sptrembl;acc:o75609] 1206 1.02526 207.646
212.904 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] 1188 1.02582 218.402
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] 1187
212.916 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 1215 1.02514 218.268
212.918 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] 1216 1.02513 218.269
212.92 vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] 2457 1.00314 213.588
212.945 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 603 1.0605 225.829
212.971 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 1748 1.01269 215.673

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/