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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Gene Rank description expected measured final Hugo
Results: HTML CSV LaTeX Showing element 2708 to 2757 of 3206 in total
Rank
description
expected
measured
final
Hugo
2708 VERY-LONG-CHAIN ACYL-COA SYNTHETASE (EC 6.2.1.-) (VERY-LONG-CHAIN- FATTY-ACID-COA LIGASE). [SWISSPROT;Acc:O14975] 2.66927 0.553489 0.207355944 SLC27A2
2709 SIMILAR TO CG7020 GENE PRODUCT (FRAGMENT). [SPTREMBL;Acc:Q96IB4] 2.24637 0.465778 0.207346964 DIP2B
2710 DISRUPTER OF SILENCING 10. [RefSeq;Acc:NM_020368] 0.698382 0.144805 0.207343546 UTP3
2711 VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 1. [RefSeq;Acc:NM_014031] 2.22067 0.46044 0.207342829 SLC27A6
2712 DELTA(14)-STEROL REDUCTASE (EC 1.3.1.70) (C-14 STEROL REDUCTASE) (STEROL C14-REDUCTASE) (DELTA14-SR) (TRANSMEMBRANE 7 SUPERFAMILY MEMBER 2) (ANOTHER NEW GENE 1) (PUTATIVE STEROL REDUCTASE SR-1). [SWISSPROT;Acc:O76062] 0.0946679 0.0196287 0.207342721 TM7SF2
2713 LAMIN B RECEPTOR (INTEGRAL NUCLEAR ENVELOPE INNER MEMBRANE PROTEIN) (LMN2R). [SWISSPROT;Acc:Q14739] 0.11804 0.0244747 0.207342426 LBR
2714 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5; VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 2; VERY LONG-CHAIN ACYL-COA SYNTHETASE-RELATED PROTEIN; LIKELY ORTHOLOG OF MOUSE SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5. [" 2.15689 0.44721 0.207340198 SLC27A5
2715 SOLUTE CARRIER FAMILY 27 MEMBER 3; FATTY ACID TRANSPORT PROTEIN 3. [RefSeq;Acc:NM_024330] 2.11862 0.439273 0.207339211 SLC27A3
2716 1.98421 0.411399 0.207336421 no value
2717 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 4; FATTY ACID TRANSPORT PROTEIN 4. [RefSeq;Acc:NM_005094]" 2.00736 0.416194 0.207334011 SLC27A4
2718 0.446911 0.0926594 0.207333004 ABHD14A
2719 0.378961 0.0784199 0.206933959 MCTP2
2720 0.493701 0.10212 0.206845844 MCTP1
2721 NADH-UBIQUINONE OXIDOREDUCTASE SUBUNIT B17.2 (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B17.2) (CI-B17.2) (CIB17.2) (13 KDA DIFFERENTIATION-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9UI09] 0.371275 0.0767473 0.206712814 NDUFA12
2722 PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (CYCLIN). [SWISSPROT;Acc:P12004] 3.65293 0.754507 0.206548442 PCNA
2723 0.1519 0.0313747 0.206548387 no value
2724 INSULIN GENE ENHANCER PROTEIN ISL-1 (ISLET-1). [SWISSPROT;Acc:P20663] 1.93018 0.398002 0.206199422 ISL1
2725 0.525053 0.10808 0.205845886 no value
2726 ACTIVATOR OF CAMP-RESPONSIVE ELEMENT MODULATOR (CREM) IN TESTIS; LIM PROTEIN ACT. [RefSeq;Acc:NM_020482] 2.24591 0.462047 0.20572819 FHL5
2727 CYTOPLASMIC CYSTEINE CONJUGATE-BETA LYASE; GLUTAMINE-PHENYLPYRUVATE AMINOTRANSFERASE. [RefSeq;Acc:NM_004059] 0.550484 0.113234 0.205698985 CCBL1
2728 ALANINE AMINOTRANSFERASE 2; GLUTAMIC-PYRUVATE TRANSAMINASE 2. [RefSeq;Acc:NM_133443] GPT2
2729 ALANINE AMINOTRANSFERASE (EC 2.6.1.2) (GLUTAMIC--PYRUVIC TRANSAMINASE) (GPT) (GLUTAMIC--ALANINE TRANSAMINASE). [SWISSPROT;Acc:P24298] 0.470166 0.0967095 0.205692245 GPT
2730 0.42621 0.087666 0.205687337 CCBL2
2731 1.72277 0.354332 0.205675743 CRLS1
2732 SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54). [SWISSPROT;Acc:P13624] 1.17566 0.241572 0.205477774 SRP54
2733 ADP-RIBOSYLATION FACTOR GTPASE ACTIVATING PROTEIN 1 (ADP-RIBOSYLATION FACTOR 1 GTPASE ACTIVATING PROTEIN) (ARF1 GAP) (ARF1-DIRECTED GTPASE- ACTIVATING PROTEIN) (GAP PROTEIN). [SWISSPROT;Acc:Q8N6T3] 0.709572 0.145697 0.205330819 ARFGAP1
2734 VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (VAMP-1) (SYNAPTOBREVIN 1). [SWISSPROT;Acc:P23763] 0.113606 0.0233268 0.205330704 VAMP1
2735 VESICLE-ASSOCIATED MEMBRANE PROTEIN 3 (VAMP-3) (SYNAPTOBREVIN 3) (CELLUBREVIN) (CEB). [SWISSPROT;Acc:Q15836] 0.104827 0.0215242 0.205330688 VAMP3
2736 CDP-DIACYLGLYCEROL--INOSITOL 3-PHOSPHATIDYLTRANSFERASE (EC 2.7.8.11) (PHOSPHATIDYLINOSITOL SYNTHASE) (PTDINS SYNTHASE) (PI SYNTHASE). [SWISSPROT;Acc:O14735] 1.88714 0.387487 0.205330288 CDIPT
2737 VESICLE-ASSOCIATED MEMBRANE PROTEIN 2 (VAMP-2) (SYNAPTOBREVIN 2). [SWISSPROT;Acc:P19065] 0.122785 0.0252114 0.205329641 VAMP2
2738 TMEM64
2739 VESICULE-ASSOCIATED MEMBRANE PROTEIN 4 (VAMP-4). [SWISSPROT;Acc:O75379] VAMP4
2740 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q9P2I0]" 1.78474 0.366149 0.205155373 CPSF2
2741 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 4, 30KD SUBUNIT; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR, 30KD; NO ARCHES-LIKE (ZEBRAFISH) ZINC FINGER PROTEIN; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR. [RefSeq;Acc:NM_006693]" 1.77759 0.364089 0.204821697 CPSF4
2742 TRS85 HOMOLOG. [SWISSPROT;Acc:Q9Y2L5] 0.141385 0.0289586 0.204820879 KIAA1012
2743 GLUTAMATE--CYSTEINE LIGASE CATALYTIC SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS HEAVY CHAIN). [SWISSPROT;Acc:P48506] 0.135904 0.027794 0.204512008 GCLC
2744 0.543616 0.111176 PPCDC
2745 0.407712 0.0833819 0.204511763 PPCS
2746 GLUTAMATE--CYSTEINE LIGASE REGULATORY SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS LIGHT CHAIN) (GLUTAMATE--CYSTEINE LIGASE MODIFIER SUBUNIT). [SWISSPROT;Acc:P48507] 0.271808 0.0555879 0.204511641 GCLM
2747 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 2. [RefSeq;Acc:NM_023112] 0.567583 0.116023 0.204415918 OTUB2
2748 WD-REPEAT PROTEIN WDC146. [SWISSPROT;Acc:Q9C0J8] 1.63634 0.334146 0.204203283 WDR33
2749 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]" CPSF1
2750 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX HELICASE SUBUNIT (EC 3.6.1.-) (DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS) (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (CXPD) (DNA EXCISION REPAIR PROTEIN ERCC-2). [SWISSPROT;Acc:P18074] 1.87606 0.382713 0.203998273 ERCC2
2751 0.576375 0.117541 0.203931468 NARS2
2752 "ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.22) (ASPARAGINE-- TRNA LIGASE) (ASNRS). [SWISSPROT;Acc:O43776]" NARS
2753 0.486671 0.099187 0.203807089 PGAM5
2754 ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT (BETA-ETF). [SWISSPROT;Acc:P38117] 2.11091 0.429899 0.203655769 ETFB
2755 1.49161 0.303744 0.203634998 SSU72
2756 0.756695 0.153382 0.202699899 ATAD1
2757 ACETYL-COA CARBOXYLASE 1 (EC 6.4.1.2) (ACC-ALPHA) [INCLUDES: BIOTIN CARBOXYLASE (EC 6.3.4.14)]. [SWISSPROT;Acc:Q13085] 5.26987 1.06806 0.202672931 ACACA

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/