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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description expected measured Hugo final
Results: HTML CSV LaTeX Showing element 251 to 300 of 3206 in total
Rank
description
expected
measured
Hugo
final
251 2.38318 0.743299 no value 0.311893772
252 SMALL GTP-BINDING TUMOR SUPPRESSOR 1. [RefSeq;Acc:NM_145173] 0.538752 0.168031 DIRAS1 0.311889329
253 DI-RAS2. [RefSeq;Acc:NM_017594] 0.675823 0.210781 DIRAS2 0.311887876
254 1.93876 0.604572 NACAD 0.311834368
255 EXOCYST COMPLEX COMPONENT SEC10 (HSEC10). [SWISSPROT;Acc:O00471] 0.799962 0.249321 EXOC5 0.311666054
256 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 1; GAR1 PROTEIN. [RefSeq;Acc:NM_018983]" 0.363171 0.11305 NOLA1 0.311285868
257 "TRANSCRIPTION FACTOR IIIB 90 KDA SUBUNIT (TFIIIB90) (HTFIIIB90) (B- RELATED FACTOR 1) (HBRF) (TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE III, SUBUNIT 2) (TAF3B2). [SWISSPROT;Acc:Q92994]" 0.121057 0.0376832 BRF1 0.311284767
258 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 9 (EIF-3 ETA) (EIF3 P116) (EIF3 P110) (EIF3B). [SWISSPROT;Acc:P55884] 1.3435 0.416665 EIF3B 0.310133978
259 "EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA, 3. [RefSeq;Acc:NM_003760]" 2.7378 0.84511 EIF4G3 0.308682154
260 NS1-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_006372] 0.213303 0.0658169 SYNCRIP 0.308560592
261 APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 0.180015 0.0555455 no value 0.308560398
262 0.180466 0.0556846 0.308560061
263 RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027] 0.181705 0.0560669 0.308560029
264 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN R (HNRNP R). [SWISSPROT;Acc:O43390] 0.225301 0.0695188 HNRNPR 0.30855966
265 EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA (EIF-4-GAMMA) (EIF- 4G) (EIF4G) (P220). [SWISSPROT;Acc:Q04637] 2.77604 0.856237 EIF4G1 0.308438279
266 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 8 (EIF3 P110) (EIF3C). [SWISSPROT;Acc:Q99613] 1.36159 0.419259 EIF3C 0.307918683
267 0.494121 0.152054 no value 0.307726245
268 CYTOPLASMIC PROTEIN NCK2 (NCK ADAPTOR PROTEIN 2) (SH2/SH3 ADAPTOR PROTEIN NCK-BETA) (NCK-2). [SWISSPROT;Acc:O43639] 1.56343 0.480352 NCK2 0.307242409
269 SPLICING FACTOR 3B SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 130) (SAP 130) (SF3B130) (PRE-MRNA SPLICING FACTOR SF3B 130 KDA SUBUNIT). [SWISSPROT;Acc:Q15393] 3.53138 1.08194 no value 0.306378809
270 MAX PROTEIN. [SWISSPROT;Acc:P25912] 0.780188 0.239018 MAX 0.306359493
271 NADH-UBIQUINONE OXIDOREDUCTASE B22 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B22) (CI-B22). [SWISSPROT;Acc:Q9Y6M9] 0.658159 0.201492 NDUFB9 0.306144868
272 EPIDIDYMAL SECRETORY PROTEIN E1 PRECURSOR (NIEMANN-PICK DISEASE TYPE C2 PROTEIN) (EPI-1) (HE1) (EPIDIDYMAL SECRETORY PROTEIN 14.6) (ESP14.6). [SWISSPROT;Acc:Q15668] 0.377878 0.115432 NPC2 0.305474254
273 0.177846 0.0542439 TRMT6 0.305004892
274 1.03903 0.316909 C14orf172 0.305004668
275 SPLICING FACTOR 3B SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 145) (SAP 145) (SF3B150) (PRE-MRNA SPLICING FACTOR SF3B 145 KDA SUBUNIT). [SWISSPROT;Acc:Q13435] 1.82999 0.557721 SF3B2 0.304767239
276 ENTEROPEPTIDASE PRECURSOR (EC 3.4.21.9) (ENTEROKINASE). [SWISSPROT;Acc:P98073] 0.116699 0.0355659 PRSS7 0.304766108
277 HISTONE ACETYLTRANSFERASE TYPE B CATALYTIC SUBUNIT (EC 2.3.1.48). [SWISSPROT;Acc:O14929] 0.920862 0.280486 HAT1 0.304590699
278 "OLIGOPEPTIDE TRANSPORTER, KIDNEY ISOFORM (PEPTIDE TRANSPORTER 2) (KIDNEY H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 2). [SWISSPROT;Acc:Q16348]" 1.10122 0.33474 SLC15A2 0.303971958
279 CYTOPLASMIC PROTEIN NCK1 (NCK ADAPTOR PROTEIN 1) (SH2/SH3 ADAPTOR PROTEIN NCK-ALPHA). [SWISSPROT;Acc:P16333] 1.77667 0.539996 NCK1 0.303937141
280 "OLIGOPEPTIDE TRANSPORTER, SMALL INTESTINE ISOFORM (PEPTIDE TRANSPORTER 1) (INTESTINAL H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 1). [SWISSPROT;Acc:P46059]" 0.807655 0.245451 SLC15A1 0.303905752
281 RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN 65KDA; RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN (65KD); RETINITIS PIGMENTOSA 20 (AUTOSOMAL RECESSIVE). [RefSeq;Acc:NM_000329] 0.141553 0.0427222 RPE65 0.301810629
282 "FATTY ACID-BINDING PROTEIN, BRAIN (B-FABP) (BRAIN LIPID-BINDING PROTEIN) (BLBP) (MAMMARY DERIVED GROWTH INHIBITOR RELATED). [SWISSPROT;Acc:O15540]" 0.127753 0.0385572 FABP7 0.301810525
283 "BETA-CAROTENE 15, 15'-DIOXYGENASE; BETA-CAROTENE 15,15'-MONOOXYGENASE. [RefSeq;Acc:NM_017429]" 0.182179 0.0549835 BCMO1 0.301810307
284 WD-REPEAT PROTEIN 4. [SWISSPROT;Acc:P57081] WDR4
285 INDOLETHYLAMINE N-METHYLTRANSFERASE (EC 2.1.1.49) (AROMATIC ALKYLAMINE N-METHYLTRANSFERASE) (INDOLAMINE N-METHYLTRANSFERASE) (ARYLAMINE N- METHYLTRANSFERASE) (AMINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:O95050] INMT
286 "FATTY ACID-BINDING PROTEIN, HEART (H-FABP) (MUSCLE FATTY ACID-BINDING PROTEIN) (M-FABP) (MAMMARY-DERIVED GROWTH INHIBITOR) (MDGI). [SWISSPROT;Acc:P05413]" 0.153258 0.0462548 FABP3 0.30181002
287 "FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 0.110947 0.0334849 no value 0.301809873
288 MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689] 0.123882 0.0373888 PMP2 0.301809787
289 0.181906 0.054901 C10orf58 0.301809726
290 0.144696 0.0436706 NXNL1 0.301809311
291 KELCH-LIKE PROTEIN 8. [SWISSPROT;Acc:Q9P2G9] 7.19846 2.17256 KLHL8 0.301808998
292 "FATTY ACID-BINDING PROTEIN, ADIPOCYTE (AFABP) (ADIPOCYTE LIPID-BINDING PROTEIN) (ALBP) (A-FABP). [SWISSPROT;Acc:P15090]" 0.12452 0.0375812 FABP4 0.301808545
293 PHENYLETHANOLAMINE N-METHYLTRANSFERASE (EC 2.1.1.28) (PNMTASE) (NORADRENALINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:P11086] 0.144924 0.0437393 PNMT 0.301808534
294 "BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 0.142328 0.0429558 no value 0.301808499
295 1.02794 0.310048 EFHC2 0.301620717
296 BAI1-ASSOCIATED PROTEIN 1; WW DOMAIN-CONTAINING PROTEIN 3; ATROPHIN-1 INTERACTING PROTEIN 3. [RefSeq;Acc:NM_004742] 0.60884 0.183128 MAGI1 0.300781815
297 ATROPHIN-1 INTERACTING PROTEIN 1; ACTIVIN RECEPTOR INTERACTING PROTEIN 1; LIKELY ORTHOLOG OF MOUSE ACTIVIN RECEPTOR INTERACTING PROTEIN 1; ATROPHIN-1 INTERACTING PROTEIN A; MEMBRANE ASSOCIATED GUANYLATE KINASE 2; ACTIVIN RECEPTOR INTERACTING P. [Re 0.756337 0.227252 MAGI2 0.300463947
298 SPLICING FACTOR 3A SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 62) (SAP 62) (SF3A66). [SWISSPROT;Acc:Q15428] 1.24681 0.374541 SF3A2 0.300399419
299 KRUEPPEL-LIKE FACTOR 5 (INTESTINAL-ENRICHED KRUEPPEL-LIKE FACTOR) (COLON KRUEPPEL-LIKE FACTOR) (TRANSCRIPTION FACTOR BTEB2) (BASIC TRANSCRIPTION ELEMENT BINDING PROTEIN 2) (BTE-BINDING PROTEIN 2) (GC BOX BINDING PROTEIN 2). [SWISSPROT;Acc:Q13887] 0.138666 0.0416551 KLF5 0.3003988
300 "CALPAIN 2, LARGE [CATALYTIC] SUBUNIT PRECURSOR (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (M-TYPE) (M-CALPAIN) (MILLIMOLAR-CALPAIN) (CALPAIN LARGE POLYPEPTIDE L2). [SWISSPROT;Acc:P17655]" 0.672496 0.201663 CAPN2 0.299872416

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/