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.


Navigation/Query Panel:
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measured Hugo Rank Gene expected description final
Results: HTML CSV LaTeX Showing element 401 to 450 of 3206 in total
measured
Hugo
Rank
expected
description
final
0.0337015 RPAP1 2461 0.155511 0.216714573
TADA3L 2463 TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [RefSeq;Acc:NM_006354]
0.0337208 NHP2L1 397 0.121119 NHP2-LIKE PROTEIN 1 (HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG 1) ([U4/U6.U5] TRI-SNRNP 15.5 KDA PROTEIN) (OTK27). [SWISSPROT;Acc:P55769] 0.278410489
0.0337232 IGBP1 1599 0.140465 IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [SWISSPROT;Acc:P78318] 0.240082583
0.0337699 REXO2 949 0.131705 "OLIGORIBONUCLEASE, MITOCHONDRIAL PRECURSOR (EC 3.1.-.-) (SMALL FRAGMENT NUCLEASE) (CGI-114). [SWISSPROT;Acc:Q9Y3B8]" 0.256405603
0.0337842 ARFGEF1 1494 0.139157 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1 (BREFELDIN A-INHIBITED GEP 1) (P200 ARF-GEP1) (P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR). [SWISSPROT;Acc:Q9Y6D6] 0.242777582
0.0338352 FKBP1A 1519 0.13962 FK506-BINDING PROTEIN 1A (EC 5.2.1.8) (PEPTIDYL-PROLYL CIS-TRANS ISOMERASE) (PPIASE) (ROTAMASE) (12 KDA FKBP) (FKBP-12) (IMMUNOPHILIN FKBP12). [SWISSPROT;Acc:P20071] 0.242337774
SOCS1 1518 SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS-1) (JAK-BINDING PROTEIN) (JAB) (STAT INDUCED STAT INHIBITOR 1) (SSI-1) (TEC-INTERACTING PROTEIN 3) (TIP-3). [SWISSPROT;Acc:O15524]
0.0338955 ASNSD1 1699 0.142498 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] 0.237866496
0.0339667 AQR 1259 0.137332 0.247332741
0.0340138 ADCK1 1651 0.142333 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421] 0.238973393
ADCK2 1652 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853]
CABC1 1650 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]"
0.0340698 SNRPB2 1104 0.135722 "U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B"". [SWISSPROT;Acc:P08579]" 0.251026363
0.0341617 KCMF1 493 0.12454 "POTASSIUM CHANNEL MODULATORY FACTOR 1; POTASSIUM CHANNEL MODULATORY FACTOR; DIFFERENTIALLY EXPRESSED IN BRANCHING TUBULOGENESIS 91; ZINC FINGER, ZZ DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020122]" 0.274303035
0.0341846 SPTBN2 592 0.126926 "SPECTRIN BETA CHAIN, BRAIN 2 (SPECTRIN, NON-ERYTHROID BETA CHAIN 2) (BETA-III SPECTRIN). [SWISSPROT;Acc:O15020]" 0.269327009
0.0341996 MARCH8 1874 0.146922 CELLULAR MODULATOR OF IMMUNE RECOGNITION. [RefSeq;Acc:NM_145021] 0.232773853
0.0342505 TCP11 2124 0.150141 T-COMPLEX 11. [RefSeq;Acc:NM_018679] 0.228122232
0.034272 no value 373 0.122748 0.279206179
0.034279 GSK3B 1378 0.140116 GLYCOGEN SYNTHASE KINASE-3 BETA (EC 2.7.1.37) (GSK-3 BETA). [SWISSPROT;Acc:P49841] 0.244647292
0.0342868 CSE1L 1072 0.135906 IMPORTIN-ALPHA RE-EXPORTER (CHROMOSOME SEGREGATION 1-LIKE PROTEIN) (CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN). [SWISSPROT;Acc:P55060] 0.252283196
0.0342893 NKIRAS2 1272 0.139064 I-KAPPA-B-INTERACTING RAS-LIKE PROTEIN 2. [RefSeq;Acc:NM_017595] 0.246572082
0.0343037 C20orf42 2511 0.159725 0.214767256
0.0343914 TMBIM4 2154 0.151289 Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24] 0.227322542
0.0344025 PCDH15 2358 0.156164 PROTOCADHERIN 15 PRECURSOR. [SWISSPROT;Acc:Q96QU1] 0.220297252
0.0344093 MLYCD 831 0.131824 "MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 4.1.1.9) (MCD). [SWISSPROT;Acc:O95822]" 0.261024548
0.0344183 PDCL 1054 0.136218 PHOSDUCIN-LIKE PROTEIN (PHLP). [SWISSPROT;Acc:Q13371] 0.252670719
RAD52 1055 DNA REPAIR PROTEIN RAD52 HOMOLOG. [SWISSPROT;Acc:P43351]
0.0344618 no value 492 0.125634 0.274303135
ARFGAP3 491 ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61]
CHCHD6 490
0.0345092 PIK3C2A 881 0.132688 "PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [RefSeq;Acc:NM_002645]" 0.260077776
0.0346049 SETD3 2436 0.159272 0.2172692
0.0348108 SCOC 931 0.135208 SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547] 0.257461097
0.0349396 UBE2W 1078 0.138505 0.252262373
0.0349473 ABT1 987 0.136958 ACTIVATOR OF BASAL TRANSCRIPTION 1; TATA-BINDING PROTEIN-BINDING PROTEIN; BASAL TRANSCRIPTIONAL ACTIVATOR. [RefSeq;Acc:NM_013375] 0.255168008
0.0349547 SLC37A2 912 0.135465 0.258034917
0.0349958 SRPK2 1338 0.142675 SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691] 0.245283336
0.0350787 AMMECR1 2177 0.154573 AMMECR1 PROTEIN. [RefSeq;Acc:NM_015365] 0.226939375
RAE1 2176 MRNA-ASSOCIATED PROTEIN MRNP 41 (RAE1 PROTEIN HOMOLOG). [SWISSPROT;Acc:P78406]
SCYL1 2174 SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680]
TMF1 2175 TATA ELEMENT MODULATORY FACTOR (TMF). [SWISSPROT;Acc:P82094]
0.035086 NEK1 1690 0.147362 SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6] 0.238093946
0.0355659 PRSS7 276 0.116699 ENTEROPEPTIDASE PRECURSOR (EC 3.4.21.9) (ENTEROKINASE). [SWISSPROT;Acc:P98073] 0.304766108
0.0355674 RAB11FIP2 767 0.134909 0.263639935
0.035571 HOXB5 2979 0.254881 HOMEOBOX PROTEIN HOX-B5 (HOX-2A) (HHO.C10) (HU-1). [SWISSPROT;Acc:P09067] 0.139559245
0.0356563 CLGN 1049 0.14106 CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967] 0.252773997
0.035822 SMOC2 660 0.134108 SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138] 0.267113073
0.0358609 LRRC4B 540 0.13229 0.271077935
0.0359383 SCAMP3 2654 0.171181 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828] 0.209943276

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/