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 measured final description Hugo expected
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
Rank
measured
final
description
Hugo
expected
3158 0.0741473 0.064710559 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 1 (MYOSIN HEAVY CHAIN IIX/D) (MYHC-IIX/D). [SWISSPROT;Acc:P12882]" MYH1 1.14583
3159 0.0736775 0.064710558 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, PERINATAL (MYHC-PERINATAL). [SWISSPROT;Acc:P13535]" MYH8 1.13857
3160 0.0681828 0.064710438 DJ756N5.1.1 (CONTINUES IN EM:AL133324 AS DJ1161H23.3) (FRAGMENT). [SPTREMBL;Acc:Q9H430] MYH7B 1.05366
3161 0.0720434 0.064710416 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, EXTRAOCULAR (MYHC-EO). [SWISSPROT;Acc:Q9UKX3]" MYH13 1.11332
3162 0.0727992 0.0647104 "MYOSIN HEAVY CHAIN, FAST SKELETAL MUSCLE, EMBRYONIC (MUSCLE EMBRYONIC MYOSIN HEAVY CHAIN) (SMHCE). [SWISSPROT;Acc:P11055]" MYH3 1.125
3163 0.0816437 0.064710307 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" no value 1.26168
3164 0.0739839 0.064710271 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 2 (MYOSIN HEAVY CHAIN IIA) (MYHC-IIA). [SWISSPROT;Acc:Q9UKX2]" MYH2 1.14331
3165 0.0736571 0.06471026 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, FETAL (MYOSIN HEAVY CHAIN IIB) (MYHC-IIB). [SWISSPROT;Acc:Q9Y623]" MYH4 1.13826
3166 0.081705 0.064710168 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" no value 1.26263
3167 0.73655 0.06471012 C5orf33 11.3823
3168 0.0509886 0.062788507 "RIBOSOMAL PROTEIN S6 KINASE, 52KDA, POLYPEPTIDE 1; RIBOSOMAL PROTEIN S6 KINASE, 52KD, POLYPEPTIDE 1. [RefSeq;Acc:NM_012424]" RPS6KC1 0.812069
3169 0.038917 0.062788394 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] no value 0.619812
3170 0.0287078 0.059152434 "T-COMPLEX PROTEIN 1, GAMMA SUBUNIT (TCP-1-GAMMA) (CCT-GAMMA). [SWISSPROT;Acc:P49368]" CCT3 0.485319
3171 0.0439931 0.05906224 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN. [SWISSPROT;Acc:O94903] PROSC 0.74486
3172 0.057781 0.055582704 NUCLEAR RNA EXPORT FACTOR 1 (TIP ASSOCIATING PROTEIN) (TIP-ASSOCIATED PROTEIN) (MRNA EXPORT FACTOR TAP). [SWISSPROT;Acc:Q9UBU9] NXF1 1.03955
3173 0.0469672 0.055483206 NUCLEAR RNA EXPORT FACTOR 3 (TAP-LIKE PROTEIN 3) (TAPL-3). [SWISSPROT;Acc:Q9H4D5] NXF3 0.846512
3174 0.0455028 0.055466395 NUCLEAR RNA EXPORT FACTOR 5 (TAP-LIKE PROTEIN 1) (TAPL-1). [SWISSPROT;Acc:Q9H1B4] NXF5 0.820367
3175 0.0184372 0.055311655 NIPA2 0.333333
3176 C6orf130
3177 PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172] UBAC1
3178 0.145007 0.049776531 S-PHASE KINASE-ASSOCIATED PROTEIN 1A (CYCLIN A/CDK2-ASSOCIATED PROTEIN P19) (P19A) (P19SKP1) (RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN) (ORGAN OF CORTI PROTEIN 2) (OCP-II PROTEIN) (OCP-2) (TRANSCRIPTION ELONGATION FACTOR B) (SIII). [SWISSPR SKP1A 2.91316
3179 0.0313105 0.049776478 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] CUL1 0.629022
3180 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768] PSEN1
3181 0.0241952 0.049776476 CULLIN HOMOLOG 2 (CUL-2). [SWISSPROT;Acc:Q13617] CUL2 0.486077
3182 0.0883895 0.04977643 "F-BOX PROTEIN FBW7 ISOFORM 2; ARCHIPELAGO, DROSOPHILA, HOMOLOG OF; F-BOX PROTEIN FBW7; F-BOX PROTEIN SEL-10; HOMOLOG OF C ELEGANS SEL-10. [RefSeq;Acc:NM_018315]" FBXW7 1.77573
3183 0.0257685 0.049776408 PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810] PSEN2 0.517685
3184 0.0656147 0.049410892 PYCRL 1.32794
3185 0.0476371 0.04678744 CCDC104 1.01816
3186 0.0311291 0.037315127 FICOLIN 2 PRECURSOR (COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2) (FICOLIN-B) (FICOLIN B) (SERUM LECTIN P35) (EBP-37) (HUCOLIN) (L- FICOLIN). [SWISSPROT;Acc:Q15485] FCN2 0.834222
3187 0.028817 0.037315105 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" no value 0.772261
3188 0.0241928 0.037315104 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14A; 17-KDA PKC-POTENTIATED INHIBITORY PROTEIN OF PP1. [RefSeq;Acc:NM_033256]" PPP1R14A 0.648338
3189 0.0318436 0.037315028 MICROFIBRIL-ASSOCIATED GLYCOPROTEIN 4 PRECURSOR. [SWISSPROT;Acc:P55083] MFAP4 0.853372
3190 0.0229678 0.037315011 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]" PPP1R14D 0.615511
3191 0.05032 0.037314982 FIBCD1 1.34852
3192 0.0142939 0.03686237 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [RefSeq;Acc:NM_020799] STAMBPL1 0.387764
3193 0.0228851 0.036862282 PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43] CHMP4A 0.620827
3194 0.0239451 0.036862264 CHMP4C 0.649583
3195 0.0179282 0.036862223 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [RefSeq;Acc:NM_006463] STAMBP 0.486357
3196 0.031557 0.036862209 CHMP4B 0.85608
3197 0.027115 0.036862168 NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079] VPS24 0.735578
3198 0.0100954 0.036862149 PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453] CHMP2A 0.273869
3199 0.00386024 0.036862138 CHMP2B 0.104721
3200 0.0391808 0.023892334 RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570] RRAGA 1.63989
3201 0.029 0.023892303 RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157] RRAGC 1.21378
3202 0.0289077 0.023892241 "ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, DROSOPHILA); ANILLIN (DROSOPHILA SCRAPS HOMOLOG), ACTIN BINDING PROTEIN. [RefSeq;Acc:NM_018685]" ANLN 1.20992
3203 0.0426192 0.023892231 RAS-RELATED GTP BINDING B SHORT ISOFORM; GTP-BINDING PROTEIN RAGB. [RefSeq;Acc:NM_006064] RRAGB 1.78381
3204 0.000178236 0.000219977 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] no value 0.81025
3205 0.000571223 0.000219976 C1orf166 2.59675
3206 0.000173011 no value 0.7865

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/