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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description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 851 to 900 of 3206 in total
description
Rank
measured
expected
final
Hugo
"SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]" 2469 0.0737619 0.340556 0.216592572 SPTBN5
"SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" 1685 0.0238444 0.100146 0.238096379 SFRS1
"SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" 638 0.280063 1.04414 0.26822361 SFRS3
"SPLICING FACTOR, ARGININE/SERINE-RICH 8 (SUPPRESSOR OF WHITE APRICOT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q12872]" 1121 0.155587 0.620608 0.250700926 SFRS8
"SPLICING FACTOR, PROLINE-AND GLUTAMINE-RICH (POLYPYRIMIDINE TRACT- BINDING PROTEIN-ASSOCIATED SPLICING FACTOR) (PTB-ASSOCIATED SPLICING FACTOR) (PSF) (DNA-BINDING P52/P100 COMPLEX, 100 KDA SUBUNIT). [SWISSPROT;Acc:P23246]" 1672 0.263446 1.10501 0.238410512 SFPQ
"STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [RefSeq;Acc:NM_015077]" 467 0.305359 1.11055 0.274961956 SARM1
"STEROID HORMONE RECEPTOR ERR1 (ESTROGEN-RELATED RECEPTOR, ALPHA) (ERR-ALPHA) (ESTROGEN RECEPTOR-LIKE 1). [SWISSPROT;Acc:P11474]" 2694 0.13519 0.649418 0.208171009 ESRRA
"STEROID HORMONE RECEPTOR ERR2 (ESTROGEN-RELATED RECEPTOR, BETA) (ERR-BETA) (ESTROGEN RECEPTOR-LIKE 2) (ERR BETA-2). [SWISSPROT;Acc:O95718]" 2706 0.175846 0.847805 0.207413261 ESRRB
"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). [SWISSPRO" 1996 0.240428 1.04189 0.230761405 SDHC
"SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 2835 0.0431276 0.223379 0.193069178 no value
"SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (FP) (FLAVOPROTEIN SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P31040]" 2053 0.150581 0.655122 0.229851844 SDHA
"SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P21912]" 2017 0.311095 1.34923 0.230572252 SDHB
"SUCCINYL-COA LIGASE [ADP-FORMING] BETA-CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.2.1.5) (SUCCINYL-COA SYNTHETASE, BETAA CHAIN) (SCS-BETAA) (ATP- SPECIFIC SUCCINYL-COA SYNTHETASE BETA SUBUNIT). [SWISSPROT;Acc:Q9P2R7]" 2390 0.245024 1.11536 0.219681538 SUCLA2
"SUCCINYL-COA LIGASE [GDP-FORMING] ALPHA-CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.2.1.4) (SUCCINYL-COA SYNTHETASE, ALPHA CHAIN) (SCS-ALPHA). [SWISSPROT;Acc:P53597]" 2389 SUCLG1
"SUPPRESSOR OF VAR1, 3-LIKE 1. [RefSeq;Acc:NM_003171]" 1379 0.0439474 0.179636 0.244646953 SUPV3L1
"SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" 1141 0.108251 0.43247 0.250308692 SMARCB1
"SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1 (SWI/SNF COMPLEX 60 KDA SUBUNIT) (BRG1- ASSOCIATED FACTOR 60A). [SWISSPROT;Acc:Q96GM5]" 388 0.140567 0.504282 0.278746812 SMARCD1
"SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1 (SWI-SNF COMPLEX PROTEIN P270) (B120). [SWISSPROT;Acc:O14497]" 113 0.182783 0.506093 0.361164845 ARID1A
"T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]" 3099 0.063706 0.673766 0.094552115 TCP1
"T-COMPLEX PROTEIN 1, DELTA SUBUNIT (TCP-1-DELTA) (CCT-DELTA) (STIMULATOR OF TAR RNA BINDING). [SWISSPROT;Acc:P50991]" 191 0.081012 0.248211 0.326383601 CCT4
"T-COMPLEX PROTEIN 1, EPSILON SUBUNIT (TCP-1-EPSILON) (CCT-EPSILON). [SWISSPROT;Acc:P48643]" 3062 0.204288 1.93831 0.105394906 CCT5
"T-COMPLEX PROTEIN 1, GAMMA SUBUNIT (TCP-1-GAMMA) (CCT-GAMMA). [SWISSPROT;Acc:P49368]" 3170 0.0287078 0.485319 0.059152434 CCT3
"TARGET OF EGR1, MEMBER 1 (NUCLEAR); TARGET OF EGR1, MEMBER 1. [RefSeq;Acc:NM_025077]" 168 0.12614 0.369099 0.341751129 TOE1
"TATA BOX BINDING PROTEIN-ASSOCIATED FACTOR, RNA POLYMERASE II, Q; TAF7-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 50 KD; TBP-ASSOCIATED FACTOR, RNA POLYMERASE II, Q. [RefSeq;Acc:NM_024885]" 354 0.103996 0.36903 0.281809067 TAF7L
"TBP-ASSOCIATED FACTOR 9L; NEURONAL CELL DEATH-RELATED PROTEIN; TAF9-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 31 KD; NEURONAL CELL DEATH-RELATED GENE IN NEURON-7; TRANSCRIPTION ASSOCIATED FACTOR TAFII31L; TRANSCRIPTION INIT" 2675 0.383112 1.83532 0.208743979 TAF9B
"TESTIS-SPECIFIC HISTONE H2B; H2B HISTONE FAMILY, MEMBER U, (TESTIS-SPECIFIC). [RefSeq;Acc:NM_170610]" 1366 0.0836563 0.341646 0.244862519 HIST1H2BA
"THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25-DIHYDROXYVITAMIN D-3. [RefSeq;Acc:NM_006472]" 1560 0.0419848 0.174068 0.241197693 TXNIP
"THIOREDOXIN, MITOCHONDRIAL PRECURSOR (MT-TRX) (THIOREDOXIN 2). [SWISSPROT;Acc:Q99757]" 1167 0.140708 0.564193 0.249396926 TXN2
"TRANSCRIPTION FACTOR CP2; TRANSCRIPTION FACTOR CP2, ALPHA GLOBIN. [RefSeq;Acc:NM_005653]" 642 0.209001 0.779209 0.268222005 TFCP2
"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]" 257 0.0376832 0.121057 0.311284767 BRF1
"TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT (TFIIF-ALPHA) (TRANSCRIPTION INITIATION FACTOR RAP74). [SWISSPROT;Acc:P35269]" 1715 0.0303013 0.127662 0.237355674 GTF2F1
"TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [RefSeq;Acc:NM_015477]" 2029 0.0283438 0.123075 0.230296973 SIN3A
"TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 1420 0.0306345 0.125605 0.243895546 TBL1X
"TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 1421 0.0303893 0.1246 0.243894864 TBL1Y
"TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL PRECURSOR (IF-2MT) (IF-2(MT)). [SWISSPROT;Acc:P46199]" 1898 0.416108 1.78993 0.232471661 MTIF2
"TRANSLOCON-ASSOCIATED PROTEIN, DELTA SUBUNIT PRECURSOR (TRAP-DELTA) (SIGNAL SEQUENCE RECEPTOR DELTA SUBUNIT) (SSR-DELTA). [SWISSPROT;Acc:P51571]" 2838 0.12066 0.62496 0.193068356 SSR4
"TREHALASE PRECURSOR (EC 3.2.1.28) (ALPHA,ALPHA-TREHALASE) (ALPHA,ALPHA-TREHALOSE GLUCOHYDROLASE). [SWISSPROT;Acc:O43280]" 2858 0.0811667 0.428605 0.189374132 TREH
"TRIACYLGLYCEROL LIPASE, GASTRIC PRECURSOR (EC 3.1.1.3) (GASTRIC LIPASE) (GL). [SWISSPROT;Acc:P07098]" 1850 0.0275767 0.118126 0.233451569 LIPF
"TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [SWISSPROT;Acc:Q9NVH6]" 469 0.218407 0.794482 0.274904907 TMLHE
"TRYPTOPHAN 2,3-DIOXYGENASE (EC 1.13.11.11) (TRYPTOPHAN PYRROLASE) (TRYPTOPHANASE) (TRYPTOPHAN OXYGENASE) (TRYPTAMIN 2,3-DIOXYGENASE) (TRPO). [SWISSPROT;Acc:P48775]" 676 0.157338 0.591312 0.26608288 TDO2
"TRYPTOPHANYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.2) (TRYPTOPHAN--TRNA LIGASE) (TRPRS) ((MT)TRPRS). [SWISSPROT;Acc:Q9UGM6]" 2370 0.0775947 0.352624 0.220049401 WARS2
"TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 1, ENDOTHELIAL (B12 PROTEIN). [SWISSPROT;Acc:Q13829]" 1142 0.281828 1.12603 0.250284628 TNFAIP1
"TYROSINASE-RELATED GENE SEGMENT, EXON 5 (FRAGMENT). [SPTREMBL;Acc:Q15677]" 1138 0.0959848 0.383295 0.250420172 TYRL
"U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B"". [SWISSPROT;Acc:P08579]" 1104 0.0340698 0.135722 0.251026363 SNRPB2
"UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [SWISSPROT;Acc:P31930]" 2498 0.167149 0.776201 0.215342418 UQCRC1
"UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2) (RIESKE IRON-SULFUR PROTEIN) (RISP). [SWISSPROT;Acc:P47985]" 1905 0.102272 0.440396 0.232227359 UQCRFSL1
"UBIQUITIN-ACTIVATING ENZYME E1C (UBA3 HOMOLOG, YEAST); UBIQUITIN-ACTIVATING ENZYME E1C (HOMOLOGOUS TO YEAST UBA3). [RefSeq;Acc:NM_003968]" 2594 0.0734554 0.345038 0.212890754 UBE1C
"UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; 1 ALPHA,25-DIHYDROXYVITAMIN D3-INDUCIBLE; ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR; METHYL METHANESULFONATE SENSITIVE 2, S. CEREVISIAE, HOMOLOG OF. [RefSeq;Acc:NM_003350]" 1612 0.274194 1.14341 0.239803745 UBE2V2
"URACIL-DNA GLYCOSYLASE, MITOCHONDRIAL PRECURSOR (EC 3.2.2.-) (UDG). [SWISSPROT;Acc:P13051]" 1739 0.0946707 0.399507 0.236968814 UNG
"VACUOLAR ATP SYNTHASE CATALYTIC SUBUNIT A, UBIQUITOUS ISOFORM (EC 3.6.3.14) (V-ATPASE A SUBUNIT 1) (VACUOLAR PROTON PUMP ALPHA SUBUNIT 1) (V-ATPASE 69 KDA SUBUNIT 1) (ISOFORM VA68). [SWISSPROT;Acc:P38606]" 1698 0.712561 2.99562 0.23786762 ATP6V1A

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/